US20140329889A1

US20140329889A1 - Cyclic di-nucleotide induction of type i interferon

Info

Publication number: US20140329889A1
Application number: US14/268,967
Authority: US
Inventors: Russell E. Vance; Ming C. Hammond; Dara Burdette; Ellie J. Diner; Stephen C. Wilson
Original assignee: University of California
Current assignee: University of California
Priority date: 2013-05-03
Filing date: 2014-05-02
Publication date: 2014-11-06
Also published as: JP2016518140A; EP2992000A4; EP2992000B1; ES2822584T3; CN105377867A; CN105377867B; JP2021074025A; US11873319B2; US20190292216A1; WO2014179760A1; EP2992000A1; US20220081464A1; JP2019068829A

Abstract

Methods and compositions are provided for increasing the production of a type I interferon (IFN) in a cell. Aspects of the methods include increasing the level of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide in a cell in a manner sufficient to increase production of the type I interferon (IFN) by the cell. Also provided are compositions and kits for practicing the embodiments of the methods.

Description

CROSS REFERENCE TO RELATED APPLICATIONS

Under 35 U.S.C. §119(e), this application claims priority to the filing date of U.S. Provisional Patent Application Ser. No. 61/819,499, filed on May 3, 2013; the disclosure of which applications are incorporated herein by reference.

GOVERNMENT RIGHTS

This invention was made with government support under grant nos. A1063302, A1075038, A1080749, A1082357, and OD008677 awarded by the National Institutes of Health. The government has certain rights in the invention.

INTRODUCTION

Interferons (also referred to as “IFN” or “IFNs”) are proteins having a variety of biological activities, some of which are antiviral, immunomodulating and antiproliferative. They are relatively small, species-specific, single chain polypeptides, produced by mammalian cells in response to exposure to a variety of inducers such as viruses, polypeptides, mitogens and the like. Interferons protect animal tissues and cells against viral attack and are an important host defense mechanism. In most cases, interferons provide better protection to tissues and cells of the kind from which they have been produced than to other types of tissues and cells, indicating that human-derived interferon could be more efficacious in treating human diseases than interferons from other species. Interferons may be classified as Type-I, Type-II and Type-Ill interferons. Mammalian Type-I interferons include IFN-α (alpha), IFN-β (beta), IFN-κ (kappa), IFN-δ (delta), IFN-ε (epsilon), IFN-τ (tau), IFN-ω(omega), and IFN-ζ (zeta, also known as limitin).
Agents that induce interferon production find use as vaccine adjuvants and in formulations that initiate effector and memory T-cell responses. Effective adjuvants enhance specific immune responses to antigens while minimizing toxic side effects, reducing the dose and dosage of vaccinations, and broadening the immune response. There remains a need for effective adjuvants that may be coformulated with antigens derived from intracellular pathogens and cancer cells to activate an effective cellular and humoral immune response to treat intracellular pathogens and reduce tumor burden. The immunomodulatory activity of interferon proteins, and the signaling pathways that regulate interferon production, are drawing interest as a target for designing new adjuvants.
Interferons have potential in the treatment of a large number of human cancers since these molecules have anti-cancer activity that acts at multiple levels. First, interferon proteins can directly inhibit the proliferation of human tumor cells. The anti-proliferative activity is also synergistic with a variety of approved chemotherapeutic agents such as cisplatin, 5FU and paclitaxel. Secondly, the immunomodulatory activity of interferon proteins can lead to the induction of an anti-tumor immune response. This response includes activation of NK cells, stimulation of macrophage activity and induction of MHC class I surface expression, leading to the induction of anti-tumor cytotoxic T lymphocyte activity. In addition, interferons play a role in cross-presentation of antigens in the immune system. Moreover, some studies further indicate that IFN-β protein may have anti-angiogenic activity. Angiogenesis, new blood vessel formation, is critical for the growth of solid tumors. Evidence indicates that IFN-β may inhibit angiogenesis by inhibiting the expression of pro-angiogenic factors such as bFGF and VEGF. Lastly, interferon proteins may inhibit tumor invasiveness by modulating the expression of enzymes, such as collagenase and elastase, which are important in tissue remodeling.
Interferons also appear to have antiviral activities that are based on two different mechanisms. For instance, type I interferon proteins (α and β) can directly inhibit the replication of human hepatitis B virus (“HBV”) and hepatitis C virus (“HCV”), but can also stimulate an immune response that attacks cells infected with these viruses.

SUMMARY

Methods and compositions are provided for increasing the production of a type I interferon (IFN) in a cell. Aspects of the methods include increasing the level of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide in a cell in a manner sufficient to increase production of the type I interferon (IFN) by the cell. Also provided are compositions and kits for practicing the subject methods.
In one aspect, provided herein is a method for increasing the production of a type I interferon (IFN) in a cell by increasing the level of a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide in the cell in a manner sufficient to increase production of the type I interferon (IFN) by the cell.
In certain embodiments, the method includes the step of contacting the cell with the cyclic-di-nucleotide. In certain embodiments, the cyclic-di-nucleotide has two 2′-5′ phosphodiester linkages. In other embodiments, the cyclic-di-nucleotide has a 2′-5′ phosphodiester linkage and a 3′-5′ phosphodiester linkage.
In certain embodiments, the cyclic-di-nucleotide comprises a guanosine nucleoside. In some embodiments, the cyclic-di-nucleotide contains two guanosine nucleosides. In certain embodiments, the cyclic-di-nucleotide comprises an adenosine nucleoside. In some embodiments, the cyclic-di-nucleotide contains two adenosine nucleosides. In other embodiments, the cyclic-di-nucleotide comprises an adenosine nucleoside and a guanosine nucleoside.
In certain embodiments, the cyclic-di-nucleotide has the following formula:
wherein X and Y are each:
In some embodiments, the cyclic-di-nucleotide has the following formula:
In certain embodiments of the method, the level of the cyclic-di-nucleotide is increased by increasing the activity of a cGAMP synthase (cGAS) in the cell. In some embodiments, the activity of the cGAS is increased by enhancing expression of a nucleic acid encoding cGAS. In some embodiments, the activity of the cGAS is increased by introducing a nucleic acid encoding the cGAS into the cell.
In certain embodiments, the method is for increasing the production of interferon (IFN) alpha. In other embodiments, the IFN is interferon beta.
In certain embodiments, the method is for increasing the production of a type I interferon (IFN) in a mammalian cell. In particular embodiments, mammalian cell is a human cell. In some embodiments, the cell is in vitro. In other embodiments, the cell is in vivo.
In another aspect, provided herein is a method for increasing the production of a type I interferon (IFN) in a subject, the method includes the step of administering to the subject an amount of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide active agent effective to increase the production of the type I interferon in the subject.
The active agent can include, but is not limited to, any of the 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides described herein. In certain embodiments, the cyclic-di-nucleotide has two 2′-5′ phosphodiester linkages. In other embodiments, the cyclic-di-nucleotide has a 2′-5′ phosphodiester linkage and a 3′-5′ phosphodiester linkage.
In some embodiments, the cyclic-di-nucleotide contains a guanosine nucleoside. In certain embodiments, the cyclic-di-nucleotide contains two guanosine nucleosides. In some embodiments, the cyclic-di-nucleotide contains an adenosine nucleoside. In specific embodiments, the cyclic-di-nucleotide contains two adenosine nucleosides. In other embodiments, the cyclic-di-nucleotide contains an adenosine and a guanosine nucleoside. In some embodiments, the cyclic-di-nucleotide has the following formula:
wherein X and Y are each:
In some embodiments of the subject method, the cyclic-di-nucleotide has the following formula:
In certain embodiments, the 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide active agent includes an agent that increases cellular activity of a cGAMP synthase (cGAS). In specific embodiments, the agent comprises a nucleic acid encoding the cGAS.
In certain embodiments, the method is for increasing the production of interferon (IFN) alpha in a subject. In other embodiments, the method is for increasing the production of interferon beta in a subject.
In certain embodiments, the subject has a viral infection. In certain embodiments, the subject has a bacterial infection. In other embodiments, the subject has a neoplastic disease. In certain embodiments, the subject is mammal. In some embodiments, the mammal is a human.
In another aspect, provided herein is a method for increasing a stimulator of interferon genes (STING) mediated response in a subject, the method includes the step of administering to the subject an amount of a STING active agent effective to increase a STING mediated response in the subject. In certain embodiments, the STING mediated response is non-responsive to a cyclic-di-nucleotide having two 3′-5′ phosphodiester bonds.
The STING active agent can include, but is not limited to, any of the 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides described herein. In certain embodiments, the cyclic-di-nucleotide has two 2′-5′ phosphodiester linkages. In other embodiments, the cyclic-di-nucleotide has a 2′-5′ phosphodiester linkage and a 3′-5′ phosphodiester linkage.
In some embodiments, the cyclic-di-nucleotide contains a guanosine nucleoside. In certain embodiments, the cyclic-di-nucleotide contains two guanosine nucleosides. In some embodiments, the cyclic-di-nucleotide contains an adenosine nucleoside. In specific embodiments, the cyclic-di-nucleotide contains two adenosine nucleosides. In other embodiments, the cyclic-di-nucleotide contains an adenosine and a guanosine nucleoside. In some embodiments, the cyclic-di-nucleotide has the following formula:
wherein X and Y are each:
In some embodiments of the subject method, the cyclic-di-nucleotide has the following formula:
In certain embodiments, the STING active agent includes an agent that increases cellular activity of a cGAMP synthase (cGAS). In specific embodiments, the agent comprises a nucleic acid encoding the cGAS.
In certain embodiments, the STING active agent includes an agent that increases cellular activity of STING. In specific embodiments, the agent comprises a nucleic acid encoding the STING.
In certain embodiments, the subject has a viral infection. In certain embodiments, the subject has a bacterial infection. In other embodiments, the subject has a neoplastic disease. In certain embodiments, the subject is mammal. In some embodiments, the mammal is a human.
In another aspect, provided herein is a cyclic-di-nucleotide comprising a 2′-5′ phosphodiester linkage. Such cyclic-di-nucleotides are useful, for example, in practicing the subject methods, including, but not limited to, methods for increasing the production of a type I interferon in a cell or a subject.
In certain embodiments, the cyclic-di-nucleotide has two 2′-5′ phosphodiester linkages. In other embodiments, the cyclic-di-nucleotide has a 2′-5′ phosphodiester linkage and a 3′-5′ phosphodiester linkage.
In certain embodiments, the cyclic-di-nucleotide contains a guanosine nucleoside. In some embodiments, the cyclic-di-nucleotide contains two guanosine nucleosides. In certain embodiments, the cyclic-di-nucleotide contains an adenosine nucleoside. In some embodiments, the cyclic-di-nucleotide contains two adenosine nucleosides. In other embodiments, the cyclic-di-nucleotide contains an adenosine and a guanosine nucleoside.
In some embodiments, the cyclic-di-nucleotide has the following formula:
wherein X and Y are each:
In certain embodiments, the cyclic-di-nucleotide has the following formula:
In another aspect, provided herein is a composition containing a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotiden and a pharmaceutically acceptable carrier.
In certain embodiments, the cyclic-di-nucleotide has two 2′-5′ phosphodiester linkages. In other embodiments, the cyclic-di-nucleotide has a 2′-5′ phosphodiester linkage and a 3′-5′ phosphodiester linkage. In certain embodiments of the composition, the cyclic-di-nucleotide contains a guanosine nucleoside. In some embodiments, the cyclic-di-nucleotide contains two guanosine nucleosides. In certain embodiments, the cyclic-di-nucleotide contains an adenosine nucleoside. In some embodiments, the cyclic-di-nucleotide contains two adenosine nucleosides. In other embodiments, the cyclic-di-nucleotide contains an adenosine and a guanosine nucleoside.
In certain embodiments of the composition, the cyclic-di-nucleotide has the following formula:
wherein X and Y are each:
In certain embodiments of the composition, the cyclic-di-nucleotide has the following formula:

BRIEF DESCRIPTION OF THE FIGURES

The invention is best understood from the following detailed description when read in conjunction with the accompanying drawings. It is emphasized that, according to common practice, the various features of the drawings are not to-scale. On the contrary, the dimensions of the various features are arbitrarily expanded or reduced for clarity. Included in the drawings are the following figures:

FIGS. 1A-1F show the variable responsiveness of human STING variants to cyclic-di-nucleotides maps to arginine 232. (A) THP-1 cells were transduced with vectors encoding an shRNA targeting STING or a control shRNA. Cells were then stimulated with cyclic-di-GMP (cdG), dsDNA, cyclic-di-AMP (cdA), poly-inosine:cytosine (pI:C), or Sendai Virus, and induction of human interferon-β mRNA was assessed by quantitative reverse transcriptase PCR. (B) Western blotting confirmed that knockdown of STING was effective. (C) HEK293T cells were transfected with the indicated amounts of various mouse (m) or human (h) STING expression plasmid and then stimulated 6 h later by transfection with synthetic cdG (5 μM). GT denotes the null 1199N allele of Sting from Goldenticket (Gt) mice. STING activation was assessed by use of a co-transfected IFN-luciferase reporter construct. (D) Gt (STING-null) macrophages were transduced with retroviral vectors encoding the indicated STING alleles and were then stimulated 48 h later by transfection with cdG (5 μM) or dsDNA 70-mer oligonucleotide (0.5 μg/mL). IFN induction was measured by qRT-PCR. ND, not detected. (E) Binding assay of STING to 32P-c-di-GMP. STING proteins were expressed in HEK293T cells and cell lysates were subjected to UVcrosslinking with ³²P-cdG, and resolved by SDS-PAGE. Binding was quantified by autoradiography. Western blots of cell lysates with an anti-STING polyclonal antibody confirmed similar expression of the various STING proteins. (F) Responsiveness of mSTING to cGAMP is affected by mutations of R231. The indicated mutants were tested as in C.

FIG. 2 shows the sequence alignment of hSTING variants. hSTING was cloned from THP-1 cells compared to the reference STING allele (NCBI NP_—938023.1).

FIG. 3 shows that R232 of human STING is required for responsiveness to c-di-GMP, but not for binding of c-di-GMP. (A) 293T cells were transfected with the indicated alleles of mouse (m)STING or human (h)STING and were then stimulated with c-di-GMP (cdG). STING activity was detected by the induction of a co-transfected IFN-luciferase reporter construct and expressed as fold-induction over luciferase activity of unstimulated cells. (B) Lysates of transfected 293T cells were UV crosslinked in the presence of α32P-c-di-GMP, resolved by SDS-PAGE, and then analyzed by autoradiography. Lysates were also western blotted for STING and ACTIN as expression controls in parallel.

FIG. 4 shows that G230A and H232R are both required for optimal responsiveness to c-di-nucleotides but are not required for binding to c-di-nucleotides. (A, B) 293T cells were transfected with the indicated alleles of mouse (m)STING or human (h)STING and were then stimulated with c-di-GMP (cdG). STING activity was detected by the induction of a cotransfected IFN-luciferase reporter construct.

FIG. 5 shows that STING variants are responsive to cGAS. (A) HEK293T cells were transfected with the indicated STING alleles and with human and mouse cGAS (wt and GS>AA mutants) as indicated. STING activation was assessed by a co-transfected IFN-luciferase reporter construct. (B) HEK293T cells were transfected with the indicated STING alleles and with a mammalian expression vector encoding a cGAMP synthase (DncV) from V. cholerae. STING activation was assessed as in A. (C) In vitro enzymatically generated products of rWspR, rDncV and rcGAS were transfected into digitonin permeabilized HEK293T cells expressing the indicated mouse and human STING proteins. Chemically synthesized cyclic-di-GMP (cdG) and cGAMP were included as controls. STING activation was assessed as in A and B.

FIG. 6 shows that cGAS produces a non-canonical cyclic dinucleotide containing a 2′-5′ phosphodiester linkage. (A) Purified recombinant WspR, DncV and cGAS were mixed with α³²P-GTP or α³²P-ATP and the indicated unlabeled nucleotides. Reactions were mixed with TLC running buffer and nucleic acid species were resolved on a PEI-Cellulose TLC plate. (B) WspR, DncV and cGAS products labeled with α³²P-GTP were digested with nuclease P1 and Snake Venom Phosphodiesterase and nucleic acid species were resolved on a PEI-Cellulose TLC plate. (C) ¹H-³¹P HMBC of HPLC-purified cGAS product acquired at 600 MHz and 50° C. Critical through-bond correlations for the phosphodiester bonds are indicated. NMR elucidated structure of cGAS product is also shown.

FIGS. 7A-7D provide additional NMR analysis of the cGAS product. All data acquisition was performed in D2O and at 50° C. (A, B) Multiplicity-edited 1H-13C HSQC experiment in a 900 MHz field. Positive phased signals corresponding to methine and methyl protons are shown in green, negative phased signals corresponding to methylene protons are shown in blue. (C) ¹H-¹H COSY experiment in a 600 MHz field. (D) ¹H-¹H NOESY experiment in a 900 MHz field.

DETAILED DESCRIPTION

Methods and compositions are provided for increasing the production of a type I interferon (IFN) in a cell. Aspects of the methods include increasing the level of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide in a cell in a manner sufficient to increase production of the type I interferon (IFN) by the cell. Also provided are compositions and kits for practicing embodiments of the subject methods.
Before the present invention is described in greater detail, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.
Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.
Certain ranges are presented herein with numerical values being preceded by the term “about.” The term “about” is used herein to provide literal support for the exact number that it precedes, as well as a number that is near to or approximately the number that the term precedes. In determining whether a number is near to or approximately a specifically recited number, the near or approximating recited number may be a number which, in the context in which it is presented, provides the substantial equivalent of the specifically recited number.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, representative illustrative methods and materials are now described.
All publications and patents cited in this specification are herein incorporated by reference as if each individual publication or patent were specifically and individually indicated to be incorporated by reference and are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited. The citation of any publication is for its disclosure prior to the filing date and should not be constructed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.
It is noted that, as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly dictates otherwise. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation.
As will be apparent to those of skill in the art upon reading this disclosure, each of the individual embodiments described and illustrated herein has discrete components and features which may be readily separated from or combined with the features of any of the other several embodiments without departing from the scope or spirit of the present invention. Any recited method can be carried out in the order of events recited or in any other order which is logically possible.

Methods

As summarized above, methods of increasing the production of a type I interferon (IFN) in a cell, e.g., in vitro or in vivo are provided. By increasing type-I interferon production is meant that the subject methods increase type-I interferon production in a cell, as compared to a control. The magnitude of the increase may vary, and in some instances is 2-fold or greater, such as 5-fold or greater, including 10-fold or greater, as compared to a suitable control. As such, in some instances, the methods are methods of increasing type-I interferon production in a cell, e.g., by a magnitude of 2-fold or greater, such as 5-fold or greater, including 10-fold or greater, as compared to a suitable control. In those embodiments where, prior to practice of the methods, interferon production is not-detectable, the increase may result in detectable amounts of interferon production. Interferon production can be measured using any suitable method, including, but not limited to, vesicular stomatitis virus (VSV) challenge bioassay, enzyme-linked immunosorbent assay (ELISA) replicon based bioassays or by using a reporter gene (e.g., luciferase) cloned under regulation of a Type I interferon signaling pathway. See, e.g., Meager J. Immunol. Methods 261:21-36 (2002); Vrolijk et al. C. J. Virol. Methods 110:201-209 (2003); and Francois et al. Antimicrob Agents Chemother 49(9):3770-3775 (2005).
The methods may be used to increase the production of any type I interferon including, but not limited to: IFN-α (alpha), IFN-β (beta), IFN-κ (kappa), IFN-δ (delta), IFN-ε (epsilon), IFN-τ (tau), IFN-ω (omega), and IFN-ζ (zeta, also known as limitin). In some embodiments, the method is for increasing the production of IFN-α. In some embodiments, the method is for increasing IFN-β.
Aspects of the methods include increasing the level of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide in a cell in a manner sufficient to increase production of the type I interferon by the cell. By increasing the level of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide is meant that the subject methods increase the amount of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide as compared to a control. As demonstrated in the Experimental Section below, 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotides can increase the levels of type I interferon production. The magnitude of the increase may vary, and in some instances is 2-fold or greater, such as 5-fold or greater, including 10-fold or greater, 15-fold greater, 20-fold greater, 25-fold greater, 30-fold greater, 35-fold greater, 40-fold greater, 45-fold greater, 50-fold greater, or 100 fold greater, as compared to a suitable control.
Increasing the level of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide levels can be accomplished using a variety of different approaches. In some instances, the method includes providing a target cell with a cyclic-di-nucleotide active agent that increases 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide levels in the target cell. Cyclic-di-nucleotide active agents may vary, and include, but are not limited to: small molecules, nucleic acid, protein, and peptide agents.
In some embodiments, the cyclic-di-nucleotide active agent increases IFN-α (alpha), IFN-β (beta), IFN-κ (kappa), IFN-δ (delta), IFN-ε (epsilon), IFN-τ (tau), IFN-ω (omega), and/or IFN-ζ (zeta, also known as limitin) in a cell or subject as compared to a control that has not been contacted with the cyclic-di-nucleotide active agent. In such embodiments, the increase is from 1.5-fold increase to 50-fold increase or more, including 2-fold increase to 45-fold increase, 5-fold increase to 40-fold increase, 10-fold increase to 35-fold increase, 15-fold increase to 30-fold increase, 20-fold increase to 30-fold increase, and the like.
In some instances, the cyclic-di-nucleotide active agent is a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide or a functional analogue thereof. 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide include, but are not limited to, those 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides described herein.
As used herein “cyclic-di-nucleotide” refers to a compound containing two nucleosides (i.e., a first and second nucleoside), wherein the 2′ or 3′ carbon of each nucleoside is linked to the 5′ carbon of the other nucleoside by a phosphodiester bond. Therefore, a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide refers to a cyclic-di-nucleotide, wherein the 2′ carbon of at least the first or second nucleosides is linked to the 5′ carbon of the other nucleoside. 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide are discussed in greater detail below.
Functional analogues of 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides are those compounds that exhibit similar functional activity (e.g., increasing the production of a type I IFN) and may have a similar structure to a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide. In some instances, the functional analogue is a small molecule agent. Naturally occurring or synthetic small molecule compounds of interest include numerous chemical classes, such organic molecules, including small organic compounds having a molecular weight of more than 50 and less than about 2,500 daltons. Candidate agents comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate agents may comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Candidate agents are also found among biomolecules including peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof. Such molecules may be identified, among other ways, by employing suitable screening protocols.
In some instances, the cyclic-di-nucleotide active agent is an agent that increases the cellular activity of a cyclic GMP-AMP synthase (cGAS). As discussed in the Experimental Section, below, increasing the levels cGMP synthase (cGAS) can increase the production and/or activity of cyclic-di-nucleotide in a cell. As such, a target cell may be contacted with an agent that increases cGMP synthase production and/or cellular activity in a manner sufficient to increase the production of Type I interferon in the cell. In some embodiments, the cyclic-di-nucleotide active agent is a nucleic acid encoding a cGAS. Nucleic acids encoding various cGAS enzymes include, but are not limited to, those described in: Sun et al. Science 339(6121):786-91 and those deposited in GENBANK and assigned deposit numbers: NM_—138441.2 and NP_—612450.2 (human); NM_—173386.4 and NP_—775562.2 (mus musculus).
In certain embodiments, the nucleic acid encoding cGAS has the following sequence:

(SEQ ID NO: 01)

agcctggggttccccttcgggtcgcagactcttgtgtgcccgccagtag

tgcttggtttccaacagctgctgctggctcttcctcttgcggccttttc

ctgaaacggattcttctttcggggaacagaaagcgccagccatgcagcc

ttggcacggaaaggccatgcagagagcttccgaggccggagccactgcc

cccaaggcttccgcacggaatgccaggggcgccccgatggatcccaccg

agtctccggctgcccccgaggccgccctgcctaaggcgggaaagttcgg

ccccgccaggaagtcgggatcccggcagaaaaagagcgccccggacacc

caggagaggccgcccgtccgcgcaactggggcccgcgccaaaaaggccc

ctcagcgcgcccaggacacgcagccgtctgacgccaccagcgcccctgg

ggcagaggggctggagcctcctgcggctcgggagccggctctttccagg

gctggttcttgccgccagaggggcgcgcgctgctccacgaagccaagac

ctccgcccgggccctgggacgtgcccagccccggcctgccggtctcggc

ccccattctcgtacggagggatgcggcgcctggggcctcgaagctccgg

gcggttttggagaagttgaagctcagccgcgatgatatctccacggcgg

cggggatggtgaaaggggttgtggaccacctgctgctcagactgaagtg

cgactccgcgttcagaggcgtcgggctgctgaacaccgggagctactat

gagcacgtgaagatttctgcacctaatgaatttgatgtcatgtttaaac

tggaagtccccagaattcaactagaagaatattccaacactcgtgcata

ttactttgtgaaatttaaaagaaatccgaaagaaaatcctctgagtcag

tttttagaaggtgaaatattatcagcttctaagatgctgtcaaagttta

ggaaaatcattaaggaagaaattaacgacattaaagatacagatgtcat

catgaagaggaaaagaggagggagccctgctgtaacacttcttattagt

gaaaaaatatctgtggatataaccctggctttggaatcaaaaagtagct

ggcctgctagcacccaagaaggcctgcgcattcaaaactggctttcagc

aaaagttaggaagcaactacgactaaagccattttaccttgtacccaag

catgcaaaggaaggaaatggtttccaagaagaaacatggcggctatcct

tctctcacatcgaaaaggaaattttgaacaatcatggaaaatctaaaac

gtgctgtgaaaacaaagaagagaaatgttgcaggaaagattgtttaaaa

ctaatgaaataccttttagaacagctgaaagaaaggtttaaagacaaaa

aacatctggataaattctcttcttatcatgtgaaaactgccttctttca

cgtatgtacccagaaccctcaagacagtcagtgggaccgcaaagacctg

ggcctctgctttgataactgcgtgacatactttcttcagtgcctcagga

cagaaaaacttgagaattattttattcctgaattcaatctattctctag

caacttaattgacaaaagaagtaaggaatttctgacaaagcaaattgaa

tatgaaagaaacaatgagtttccagtttttgatgaattttgagattgta

tttttagaaagatctaagaactagagtcaccctaaatcctggagaatac

aagaaaaatttgaaaaggggccagacgctgtggctcac.

In some embodiments, the nucleic acid encoding cGAS is a nucleic acid with 40% to 99%, 45% to 99%, 50% to 99%, 55% to 99%, 60% to 99%, 65% to 99%, 70% to 99%, 75% to 99%, 80% to 99%, 85% to 99%, 90% to 99% or, 95% to 99% sequence identity with a wild type cGAS nucleic acid sequence. In some embodiments, the nucleic acid encoding cGAS is a nucleic acid with 40% to 50%, 50% to 60%, 60% to 70%, 70% to 80%, 80% to 90%, or 90 to 99% sequence identity with a wild type cGAS nucleic acid sequence. In some embodiments, the nucleic acid encoding cGAS is a nucleic acid with 40% or more, 45% or more, 50% or more, 55% or more, 60% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more or 99% or more sequence identity with a wild type cGAS nucleic acid sequence.
In some instances, the cyclic-di-nucleotide active agent is a vector containing a nucleic acid encoding cGAS. Vectors may be provided directly to the subject cells. In other words, the cells are contacted with vectors having the nucleic acid encoding the cyclic-di-nucleotide active agent(s) (e.g., a nucleic acid encoding cGAS) such that the vectors are taken up by the cells. Methods for contacting cells with nucleic acid vectors that are plasmids, such as electroporation, calcium chloride transfection, and lipofection, are well known in the art. For viral vector delivery, the cells are contacted with viral particles comprising the nucleic acid encoding the cyclic-di-nucleotide agent(s). Retroviruses, for example, lentiviruses, are particularly suitable to the method of the invention. Commonly used retroviral vectors are “defective”, i.e., unable to produce viral proteins required for productive infection. Rather, replication of the vector requires growth in a packaging cell line. To generate viral particles comprising nucleic acids of interest, the retroviral nucleic acids comprising the nucleic acid are packaged into viral capsids by a packaging cell line. Different packaging cell lines provide a different envelope protein (ecotropic, amphotropic or xenotropic) to be incorporated into the capsid, this envelope protein determining the specificity of the viral particle for the cells (ecotropic for murine and rat; amphotropic for most mammalian cell types including human, dog and mouse; and xenotropic for most mammalian cell types except murine cells). The appropriate packaging cell line may be used to ensure that the cells are targeted by the packaged viral particles. Methods of introducing the retroviral vectors comprising the nucleic acid encoding the reprogramming factors into packaging cell lines and of collecting the viral particles that are generated by the packaging lines are well known in the art.
Vectors used for providing the nucleic acids encoding the cyclic-di-nucleotide activity active agent(s) to the subject cells may include suitable promoters for driving the expression, that is, transcriptional activation, of the nucleic acid of interest. In other words, the nucleic acid of interest will be operably linked to a promoter. This may include ubiquitously acting promoters, for example, the CMV-β-actin promoter, or inducible promoters, such as promoters that are active in particular cell populations or that respond to the presence of drugs such as tetracycline. By transcriptional activation, it is intended that transcription will be increased above basal levels in the target cell by 10 fold or more, by 100 fold or more, by 1000 fold or more. In addition, vectors used for providing cyclic-di-nucleotide active agent(s) to the subject cells may include nucleic acid sequences that encode for selectable markers in the target cells, so as to identify cells that have taken up the cyclic-di-nucleotide activity active agent(s).
Cyclic-di-nucleotide active agent(s) may also be provided to cells as polypeptides. For example, in some instances the cyclic-di-nucleotide active agent is a cGAS polypeptide. Amino acid sequences of various cGAS enzymes include, but are not limited to, those described in: Sun et al. Science 339(6121):786-91 and those deposited in GENBANK and assigned deposit numbers: NM_—138441.2 and NP_—612450.2 (human); NM_—173386.4 and NP_—775562.2 (mus musculus).
In certain embodiments, the cGAS polypeptide has the following sequence:

(SEQ ID NO: 02)

MQPWHGKAMQRASEAGATAPKASARNARGAPMDPTESPAAPEAALPKAG

KFGPARKSGSRQKKSAPDTQERPPVRATGARAKKAPQRAQDTQPSDATS

APGAEGLEPPAAREPALSRAGSCRQRGARCSTKPRPPPGPWDVPSPGLP

VSAPILVRRDAAPGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLR

LKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNT

RAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDT

DVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNW

LSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGK

SKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTA

FFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNL

FSSNLIDKRSKEFLTKQIEY ERNNEFPVFDEF.

In some embodiments, the cGAS polypeptide is a polypeptide that has 40% to 99%, 45% to 99%, 50% to 99%, 55% to 99%, 60% to 99%, 65% to 99%, 70% to 99%, 75% to 99%, 80% to 99%, 85% to 99%, 90% to 99% or, 95% to 99% sequence identity with a wild type cGAS amino acid sequence. In some embodiments, the cGAS polypeptide is a polypeptide that has 40% to 50%, 50% to 60%, 60% to 70%, 70% to 80%, 80% to 90%, or 90 to 99% sequence identity with a wild type cGAS amino acid sequence. In some embodiments, the cGAS polypeptide is a polypeptide that has 40% or more, 45% or more, 50% or more, 55% or more, 60% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more or 99% or more sequence identity with a wild type cGAS amino acid sequence.
Such polypeptides may optionally be fused to a polypeptide domain that increases solubility of the product. The domain may be linked to the polypeptide through a defined protease cleavage site, e.g., a TEV sequence, which is cleaved by TEV protease. The linker may also include one or more flexible sequences, e.g., from 1 to 10 glycine residues. In some embodiments, the cleavage of the fusion protein is performed in a buffer that maintains solubility of the product, e.g., in the presence of from 0.5 to 2 M urea, in the presence of polypeptides and/or polynucleotides that increase solubility, and the like. Domains of interest include endosomolytic domains, e.g., influenza HA domain; and other polypeptides that aid in production, e.g., IF2 domain, GST domain, GRPE domain, and the like. The polypeptide may be formulated for improved stability. For example, the peptides may be PEGylated, where the polyethyleneoxy group provides for enhanced lifetime in the blood stream.
Additionally or alternatively, the cyclic-di-nucleotide active agent(s) may be fused to a polypeptide permeant domain to promote uptake by the cell. A number of permeant domains are known in the art and may be used in the non-integrating polypeptides of the present invention, including peptides, peptidomimetics, and non-peptide carriers. For example, a permeant peptide may be derived from the third alpha helix of Drosophila melanogaster transcription factor Antennapaedia, referred to as penetratin, which comprises the amino acid sequence RQIKIWFQNRRMKWKK (SEQ ID NO:03). As another example, the permeant peptide comprises the HIV-1 tat basic region amino acid sequence, which may include, for example, amino acids 49-57 of naturally-occurring tat protein. Other permeant domains include poly-arginine motifs, for example, the region of amino acids 34-56 of HIV-1 rev protein, nona-arginine, octa-arginine, and the like. (See, for example, Futaki et al. Curr Protein Pept Sci. 4(2): 87-96 (2003); and Wender et al. Proc. Natl. Acad. Sci. U.S.A 97(24):13003-8 (2000); published U.S. Patent applications 20030220334; 20030083256; 20030032593; and 20030022831, herein specifically incorporated by reference for the teachings of translocation peptides and peptoids). The nona-arginine (R9) sequence is one of the more efficient PTDs that have been characterized (Wender et al. 2000; Uemura et al. 2002). The site at which the fusion is made may be selected in order to optimize the biological activity, secretion or binding characteristics of the polypeptide. The optimal site will be determined by routine experimentation.
In practicing embodiments of the methods provided herein, an effective amount of the active agent, i.e., a cyclic-di-nucleotide active agent (such as described above), is provided in the target cell or cells. As used herein “effective amount” or “efficacious amount” means the amount of the active agent that, when contacted with the cell, e.g., by being introduced into the cell in vitro, by being administered to a subject, etc., is sufficient to result in increased levels of a cyclic-di-nucleotide in the cell. The “effective amount” will vary depending on cell and/or the organism and/or compound and or the nature of the desired outcome and/or the disease and its severity and the age, weight, etc., of the subject to be treated.
In some instances, the effective amount of the active agent is provided in the cell by contacting the cell with the active agent. Contact of the cell with the active agent may occur using any convenient protocol. The protocol may provide for in vitro or in vivo contact of the active agent with the target cell, depending on the location of the target cell. For example, where the target cell is an isolated cell, e.g., a cell in vitro (i.e., in culture), or a cell ex vivo (“ex vivo” being cells or organs are modified outside of the body, where such cells or organs are typically returned to a living body), the active agent may be introduced directly into the cell under cell culture conditions permissive of viability of the target cell. Such techniques include, but are not necessarily limited to: viral infection, transfection, conjugation, protoplast fusion, electroporation, particle gun technology, calcium phosphate precipitation, direct microinjection, viral vector delivery, and the like. The choice of method is generally dependent on the type of cell being contacted and the nature of the active agent, and the circumstances under which the transformation is taking place (e.g., in vitro, ex vivo, or in vivo). A general discussion of these methods can be found in Ausubel, et al, Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995. As another example, where the target cell or cells are part of a multicellular organism, the active agent may be administered to the organism or subject in a manner such that the agent is able to contact the target cell(s), e.g., via an in vivo protocol. By “in vivo,” it is meant in the target construct is administered to a living body of an animal.
In some embodiments, the cyclic-di-nucleotide active agent is employed to modulate c-di-AMP activity in mitotic or post-mitotic cells in vitro or ex vivo, i.e., to produce modified cells that can be reintroduced into an individual. Mitotic and post-mitotic cells of interest in these embodiments include any eukaryotic cell, e.g., pluripotent stem cells, for example, ES cells, iPS cells, and embryonic germ cells; somatic cells, for example, hematopoietic cells, fibroblasts, neurons, muscle cells, bone cells, vascular endothelial cells, gut cells, and the like, and their lineage-restricted progenitors and precursors; and neoplastic, or cancer, cells, i.e., cells demonstrating one or more properties associated with cancer cells, e.g., hyperproliferation, contact inhibition, the ability to invade other tissue, etc. In certain embodiments, the eukaryotic cells are cancer cells. In certain embodiments, the eukaryotic cells are hematopoietic cells, e.g., macrophages, NK cells, etc. Cells may be from any mammalian species, e.g., murine, rodent, canine, feline, equine, bovine, ovine, primate, human, etc. Cells may be from established cell lines or they may be primary cells, where “primary cells”, “primary cell lines”, and “primary cultures” are used interchangeably herein to refer to cells and cells cultures that have been derived from a subject and allowed to grow in vitro for a limited number of passages, i.e., splittings, of the culture. For example, primary cultures are cultures that may have been passaged 0 times, 1 time, 2 times, 4 times, 5 times, 10 times, or 15 times, but not enough times go through the crisis stage. Typically, the primary cell lines of the present invention are maintained for fewer than 10 passages in vitro.
If the cells are primary cells, they may be harvested from an individual by any convenient method. For example, blood cells, e.g., leukocytes, e.g., macrophages, may be harvested by apheresis, leukocytapheresis, density gradient separation, etc., while cells from tissues such as skin, muscle, bone marrow, spleen, liver, pancreas, lung, intestine, stomach, etc. may be harvested by biopsy. An appropriate solution may be used for dispersion or suspension of the harvested cells. Such solution will generally be a balanced salt solution, e.g., normal saline, PBS, Hank's balanced salt solution, etc., conveniently supplemented with fetal calf serum or other naturally occurring factors, in conjunction with an acceptable buffer at low concentration, generally from 5-25 mM. Convenient buffers include HEPES, phosphate buffers, lactate buffers, etc. The cells may be used immediately, or they may be stored, frozen, for long periods of time, being thawed and capable of being reused. In such cases, the cells may be frozen in 10% DMSO, 50% serum, 40% buffered medium, or some other such solution as is commonly used in the art to preserve cells at such freezing temperatures, and thawed in a manner as commonly known in the art for thawing frozen cultured cells.
The cyclic-di-nucleotide active agent(s) may be produced by eukaryotic cells or by prokaryotic cells, it may be further processed by unfolding, e.g., heat denaturation, DTT reduction, etc. and may be further refolded, using methods known in the art.
Modifications of interest that do not alter primary sequence include chemical derivatization of polypeptides, e.g., acylation, acetylation, carboxylation, amidation, etc. Also included are modifications of glycosylation, e.g., those made by modifying the glycosylation patterns of a polypeptide during its synthesis and processing or in further processing steps; e.g., by exposing the polypeptide to enzymes which affect glycosylation, such as mammalian glycosylating or deglycosylating enzymes. Also embraced are sequences that have phosphorylated amino acid residues, e.g., phosphotyrosine, phosphoserine, or phosphothreonine.
Also included in the subject invention are cyclic-di-nucleotide active agent polypeptides (e.g., cGAS polypeptides) that have been modified using ordinary molecular biological techniques and synthetic chemistry so as to improve their resistance to proteolytic degradation or to optimize solubility properties or to render them more suitable as a therapeutic agent. Analogs of such polypeptides include those containing residues other than naturally occurring L-amino acids, e.g., D-amino acids or non-naturally occurring synthetic amino acids. D-amino acids may be substituted for some or all of the amino acid residues.
The cyclic-di-nucleotide active agent (s) may be prepared by in vitro synthesis, using any suitable method. Various commercial synthetic apparatuses are available, for example, automated synthesizers by Applied Biosystems, Inc., Beckman, etc. By using synthesizers, naturally occurring amino acids may be substituted with unnatural amino acids. The particular sequence and the manner of preparation will be determined by convenience, economics, purity required, and the like.
If desired, various groups may be introduced into the peptide during synthesis or during expression, which allow for linking to other molecules or to a surface. Thus cysteines can be used to make thioethers, histidines for linking to a metal ion complex, carboxyl groups for forming amides or esters, amino groups for forming amides, and the like.
The cyclic-di-nucleotide active agent(s) may also be isolated and purified in accordance with conventional methods of recombinant synthesis. A lysate may be prepared of the expression host and the lysate purified using HPLC, exclusion chromatography, gel electrophoresis, affinity chromatography, or other purification technique. For the most part, the compositions which are used will include 20% or more by weight of the desired product, such as 75% or more by weight of the desired product, including 95% or more by weight of the desired product, and for therapeutic purposes, may be 99.5% or more by weight, in relation to contaminants related to the method of preparation of the product and its purification (where the percentages may be based upon total protein).
To modulate cyclic-di-nucleotide activity and/or production, the cyclic-di-nucleotide active agent(s)—be they small molecules (e.g., 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides) polypeptides or nucleic acids that encode cyclic-di-nucleotide active agent polypeptides (e.g., cGAS)—may be provided to the cells for a sufficient period of time, e.g., from 30 minutes to 24 hours, e.g., 1 hour, 1.5 hours, 2 hours, 2.5 hours, 3 hours, 3.5 hours 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 12 hours, 16 hours, 18 hours, 20 hours, or any other period from 30 minutes to 24 hours, which may be repeated with a frequency of every day to every 4 days, e.g., every 1.5 days, every 2 days, every 3 days, or any other frequency from about every day to about every four days. The agent(s) may be provided to the subject cells one or more times, e.g., one time, twice, three times, or more than three times, and the cells allowed to incubate with the agent(s) for some amount of time following each contacting event e.g., 16-24 hours, after which time the media is replaced with fresh media and the cells are cultured further.
In certain embodiments, two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more different cyclic-di-nucleotide active agents are provided to a cell in a manner sufficient to increase production of a type I interferon by the cell. In some instances, the active agents include two or more different 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotides. In certain embodiments, the active agents include a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide and a nucleic acid encoding cGAS or a cGAS polypeptide. In instances in which two or more different cyclic-di-nucleotide active agents are provided to the cell, i.e., a cyclic-di-nucleotide active agent cocktail, the cyclic-di-nucleotide active agent(s) may be provided simultaneously, e.g., as two cyclic-di-nucleotides delivered simultaneously or a cyclic-di-nucleotide and a vector containing a nucleic acid encoding cGAS delivered simultaneously. Alternatively, they may be provided consecutively, e.g., the first cyclic-di-nucleotide active agent being provided first, followed by the cyclic-di-nucleotide active agent, etc. or vice versa.
An effective amount of cyclic-di-nucleotide active agent(s) are provided to the cells to result in a change in cyclic-di-nucleotide levels. An effective amount of cyclic-di-nucleotide active agent is the amount to result in a 2-fold increase or more in the amount of cyclic-di-nucleotide production observed relative to a negative control, e.g., a cell contacted with an empty vector or irrelevant polypeptide. That is to say, an effective amount or dose of a cyclic-di-nucleotide active agent will result in a 2-fold increase, a 3-fold increase, a 4-fold increase or more in the amount of cyclic-di-nucleotide observed, in some instances a 5-fold increase, a 6-fold increase or more, sometimes a 7-fold or 8-fold increase or more in the amount of activity observed, e.g., an increase of 10-fold, 50-fold, or 100-fold or more, in some instances, an increase of 200-fold, 500-fold, 700-fold, or 1000-fold or more, in the amount of activity observed. The amount of activity may be measured by any suitable method. For example, the amount of interferon produced by the cell may be assessed after contact with the cyclic-di-nucleotide active agent(s), e.g., 2 hours, 4 hours, 8 hours, 12 hours, 24 hours, 36 hours, 48 hours, 72 hours or more after contact with the cyclic-di-nucleotide active agent(s).
Contacting the cells with the cyclic-di-nucleotide active agent(s) may occur in any culture media and under any culture conditions that promote the survival of the cells. For example, cells may be suspended in any appropriate nutrient medium that is convenient, such as Iscove's modified DMEM or RPMI 1640, supplemented with fetal calf serum or heat inactivated goat serum (about 5-10%), L-glutamine, a thiol, particularly 2-mercaptoethanol, and antibiotics, e.g., penicillin and streptomycin. The culture may contain growth factors to which the cells are responsive. Growth factors, as defined herein, are molecules capable of promoting survival, growth and/or differentiation of cells, either in culture or in the intact tissue, through specific effects on a transmembrane receptor. Growth factors include polypeptides and non-polypeptide factors.
Following the methods described above, a cell may be modified ex vivo to have an increase in cyclic-di-nucleotide levels. In some embodiments, it may be desirous to select for the modified cell, e.g., to create an enriched population of modified cells. Any convenient modification to the cells that marks the cells as modified with a cyclic-di-nucleotide active agent may be used. For example, a selectable marker may be inserted into the genome of the cell, so that the population of cells may be enriched for those comprising the genetic modification by separating the genetically marked cells from the remaining population. Separation may be by any convenient separation technique appropriate for the selectable marker used. For example, if a fluorescent marker has been inserted, cells may be separated by fluorescence activated cell sorting, whereas if a cell surface marker has been inserted, cells may be separated from the heterogeneous population by affinity separation techniques, e.g., magnetic separation, affinity chromatography, “panning” with an affinity reagent attached to a solid matrix, or other convenient technique. Techniques providing accurate separation include fluorescence activated cell sorters, which can have varying degrees of sophistication, such as multiple color channels, low angle and obtuse light scattering detecting channels, impedance channels, etc. The cells may be selected against dead cells by employing dyes associated with dead cells (e.g., propidium iodide). Any technique may be employed which is not unduly detrimental to the viability of the genetically modified cells.
Cell compositions that are highly enriched for cells comprising cyclic-di-nucleotide active agent(s) are achieved in this manner. By “highly enriched”, it is meant that the genetically modified cells will be 70% or more, 75% or more, 80% or more, 85% or more, 90% or more of the cell composition, for example, about 95% or more, or 98% or more of the cell composition. In other words, the composition may be a substantially pure composition of cells comprising cyclic-di-nucleotide active agent(s).
Cells comprising cyclic-di-nucleotide active agent(s) produced by the methods described herein may be used immediately. Alternatively, the cells may be frozen at liquid nitrogen temperatures and stored for long periods of time, being thawed and capable of being reused. In such cases, the cells may be frozen in 10% DMSO, 50% serum, 40% buffered medium, or some other such solution as is commonly used in the art to preserve cells at such freezing temperatures, and thawed in a manner as commonly known in the art for thawing frozen cultured cells.
The cells comprising cyclic-di-nucleotide active agent(s) may be cultured in vitro under various culture conditions. The cells may be expanded in culture, i.e., grown under conditions that promote their proliferation. Culture medium may be liquid or semi-solid, e.g., containing agar, methylcellulose, etc. The cell population may be suspended in an appropriate nutrient medium, such as Iscove's modified DMEM or RPMI 1640, normally supplemented with fetal calf serum (about 5-10%), L-glutamine, a thiol, particularly 2-mercaptoethanol, and antibiotics, e.g., penicillin and streptomycin. The culture may contain growth factors to which the regulatory T cells are responsive. Growth factors, as defined herein, are molecules capable of promoting survival, growth and/or differentiation of cells, either in culture or in the intact tissue, through specific effects on a transmembrane receptor. Growth factors include polypeptides and non-polypeptide factors.
Cells that have been modified with cyclic-di-nucleotide active agent(s) may be transplanted to a subject to treat a disease or as an antiviral, antipathogenic, or anticancer therapeutic or for biological research. The subject may be a neonate, a juvenile, or an adult. Of particular interest are mammalian subjects. Mammalian species that may be treated with the present methods include canines and felines; equines; bovines; ovines; etc. and primates, particularly humans. Animal models, particularly small mammals, e.g., murine, lagomorpha, etc., may be used for experimental investigations.
Cells may be provided to the subject alone or with a suitable substrate or matrix, e.g., to support their growth and/or organization in the tissue to which they are being transplanted. In some instances, at least 1×10³cells will be administered, for example 5×10³cells, 1×10⁴cells, 5×10⁴cells, 1×10⁵cells, 1×10⁶cells or more. The cells may be introduced to the subject via any of the following routes: parenteral, subcutaneous, intravenous, intracranial, intraspinal, intraocular, or into spinal fluid. The cells may be introduced by injection, catheter, or the like. Examples of methods for local delivery, that is, delivery to the site of injury, include, e.g., through an Ommaya reservoir, e.g., for intrathecal delivery (see, e.g., U.S. Pat. Nos. 5,222,982 and 5,385,582, incorporated herein by reference); by bolus injection, e.g., by a syringe, e.g., into a joint; by continuous infusion, e.g., by cannulation, e.g., with convection (see e.g., US Application No. 20070254842, incorporated here by reference); or by implanting a device upon which the cells have been reversibly affixed (see e.g., US Application Nos. 20080081064 and 20090196903, incorporated herein by reference).
In other aspects of the invention, the cyclic-di-nucleotide active agent(s) are employed to increase the production of type I interferon in vivo. In these in vivo embodiments, the cyclic-di-nucleotide active agent(s) are administered directly to the individual. In some embodiments, the cyclic-di-nucleotide active agent administered to the subject contains a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide.
Cyclic-di-nucleotide active agent(s) may be administered by any suitable methods for the administration of peptides, small molecules and nucleic acids to a subject. The cyclic-di-nucleotide active agent(s) can be incorporated into a variety of formulations. More particularly, the cyclic-di-nucleotide active agent(s) of the present invention can be formulated into pharmaceutical compositions by combination with appropriate pharmaceutically acceptable carriers or diluents. Pharmaceutical compositions that can be used in practicing the subject methods are described below.
In such instances, an effective amount of the cyclic-di-nucleotide active agent is administered to the subject. By an “effective amount” or a “therapeutically effective amount” of the cyclic-di-nucleotide active agent it is meant an amount that is required to reduce the severity, the duration and/or the symptoms of the disease. In some embodiments, the effective amount of a pharmaceutical composition containing a cyclic-di-nucleotide active agent, as provided herein, is between 0.025 mg/kg and 1000 mg/kg body weight of a human subject. In certain embodiments, the pharmaceutical composition is administered to a human subject at an amount of 1000 mg/kg body weight or less, 950 mg/kg body weight or less, 900 mg/kg body weight or less, 850 mg/kg body weight or less, 800 mg/kg body weight or less, 750 mg/kg body weight or less, 700 mg/kg body weight or less, 650 mg/kg body weight or less, 600 mg/kg body weight or less, 550 mg/kg body weight or less, 500 mg/kg body weight or less, 450 mg/kg body weight or less, 400 mg/kg body weight or less, 350 mg/kg body weight or less, 300 mg/kg body weight or less, 250 mg/kg body weight or less, 200 mg/kg body weight or less, 150 mg/kg body weight or less, 100 mg/kg body weight or less, 95 mg/kg body weight or less, 90 mg/kg body weight or less, 85 mg/kg body weight or less, 80 mg/kg body weight or less, 75 mg/kg body weight or less, 70 mg/kg body weight or less, or 65 mg/kg body weight or less.
In another aspect, provided herein is a method for increasing a stimulator of interferon genes (STING) mediated response in a subject, e.g., a STING mediated immune response. In certain embodiments, the method includes the step of administering to the subject an amount of a STING active agent effective to increase a STING mediated response in the subject. A “STING” mediated response refers to any response that is mediated by STING, including, but not limited to, immune responses to bacterial pathogens, viral pathogens, and eukaryotic pathogens. See, e.g., Ishikawa et al. Immunity 29: 538-550 (2008); Ishikawa et al. Nature 461: 788-792 (2009); and Sharma et al. Immunity 35: 194-207 (2011). STING also functions in certain autoimmune diseases initiated by inappropriate recognition of self DNA (see, e.g., Gall et al. Immunity 36: 120-131 (2012), as well as for the induction of adaptive immunity in response to DNA vaccines (see, e.g., Ishikawa et al. Nature 461: 788-792 (2009). By increasing a STING mediated response in a subject is meant an increase in a STING mediated response in a subject as compared to a control subject (e.g., a subject who is not administered a STING active agent). In certain embodiments, the method is for increasing a stimulator of interferon genes (STING) mediated response in a subject, wherein the STING mediated response is non-responsive to a cyclic-di-nucleotide having two 3′-5′ phosphodiester bonds (i.e., a canonical cyclic dinucleotide).
As described in the Experimental Section below, cyclic-di-nucleotides having 2′-5′ phosphodiester bonds have been shown to activate STING signaling. Moreover, such cyclic-di-nucleotides having 2′-5′ phosphodiester bonds have been shown to stimulate alleles of STING that are non-responsive to cyclic-di-nucleotides that have two phosphodiester bonds. As such, in some embodiments, the STING active agent is a cyclic-di-nucleotide active agent described herein (e.g., cyclic-di-nucleotide, nucleic acid encoding cGAS).
In other embodiments the STING active agent is a nucleic acid encoding STING or a STING polypeptide. Nucleic acids encoding various STINGs include, but are not limited to, those described in: Nitta et al. Hepatology 57(1): 46-58 (2013) and Jin et al. J. Immunol. 190(6): 2835-2843 (2013) and those deposited in GENBANK and assigned deposit numbers: NM_—198282.2 and NP_—938023.1 (human); NM_—028261.1 and NP_—082537.1 (mus musculus); and NM_—057386.4 and NP_—476734.1 (Drosophila melanogaster).
In certain embodiments, the nucleic acid encoding STING has the following sequence:

(SEQ ID NO: 04)

gttcatttttcactcctccctcctaggtcacacttttcagaaaaagaat

ctgcatcctggaaaccagaagaaaaatatgagacggggaatcatcgtgt

gatgtgtgtgctgcctttggctgagtgtgtggagtcctgctcaggtgtt

aggtacagtgtgtttgatcgtggtggcttgaggggaacccgctgttcag

agctgtgactgcggctgcactcagagaagctgcccttggctgctcgtag

cgccgggccttctctcctcgtcatcatccagagcagccagtgtccggga

ggcagaagatgccccactccagcctgcatccatccatcccgtgtcccag

gggtcacggggcccagaaggcagccttggttctgctgagtgcctgcctg

gtgaccctttgggggctaggagagccaccagagcacactctccggtacc

tggtgctccacctagcctccctgcagctgggactgctgttaaacggggt

ctgcagcctggctgaggagctgcgccacatccactccaggtaccggggc

agctactggaggactgtgcgggcctgcctgggctgccccctccgccgtg

gggccctgttgctgctgtccatctatttctactactccctcccaaatgc

ggtcggcccgcccttcacttggatgcttgccctcctgggcctctcgcag

gcactgaacatcctcctgggcctcaagggcctggccccagctgagatct

ctgcagtgtgtgaaaaagggaatttcaacgtggcccatgggctggcatg

gtcatattacatcggatatctgcggctgatcctgccagagctccaggcc

cggattcgaacttacaatcagcattacaacaacctgctacggggtgcag

tgagccagcggctgtatattctcctcccattggactgtggggtgcctga

taacctgagtatggctgaccccaacattcgcttcctggataaactgccc

cagcagaccggtgaccatgctggcatcaaggatcgggtttacagcaaca

gcatctatgagcttctggagaacgggcagcgggcgggcacctgtgtcct

ggagtacgccacccccttgcagactttgtttgccatgtcacaatacagt

caagctggctttagccgggaggataggcttgagcaggccaaactcttct

gccggacacttgaggacatcctggcagatgcccctgagtctcagaacaa

ctgccgcctcattgcctaccaggaacctgcagatgacagcagcttctcg

ctgtcccaggaggttctccggcacctgcggcaggaggaaaaggaagagg

ttactgtgggcagcttgaagacctcagcggtgcccagtacctccacgat

gtcccaagagcctgagctcctcatcagtggaatggaaaagcccctccct

ctccgcacggatttctcttgagacccagggtcaccaggccagagcctcc

agtggtctccaagcctctggactgggggctctcttcagtggctgaatgt

ccagcagagctatttccttccacagggggccttgcagggaagggtccag

gacttgacatcttaagatgcgtcttgtccccttgggccagtcatttccc

ctctctgagcctcggtgtcttcaacctgtgaaatgggatcataatcact

gccttacctccctcacggttgttgtgaggactgagtgtgtggaagtttt

tcataaactttggatgctagtgtacttagggggtgtgccaggtgtcttt

catggggccttccagacccactccccacccttctccccttcctttgccc

ggggacgccgaactctctcaatggtatcaacaggctccttcgccctctg

gctcctggtcatgttccattattggggagccccagcagaagaatggaga

ggaggaggaggctgagtttggggtattgaatcccccggctcccaccctg

cagcatcaaggttgctatggactctcctgccgggcaactcttgcgtaat

catgactatctctaggattctggcaccacttccttccctggccccttaa

gcctagctgtgtatcggcacccccaccccactagagtactccctctcac

ttgcggtttccttatactccacccctttctcaacggtccttttttaaag

cacatctcagattacccaaaaaaaaaaaaaaaaaa.

In some embodiments, the nucleic acid encoding STING is a nucleic acid with 40% to 99%, 45% to 99%, 50% to 99%, 55% to 99%, 60% to 99%, 65% to 99%, 70% to 99%, 75% to 99%, 80% to 99%, 85% to 99%, 90% to 99% or, 95% to 99% sequence identity with a wild type STING nucleic acid sequence. In some embodiments, the nucleic acid encoding STING is a nucleic acid with 40% to 50%, 50% to 60%, 60% to 70%, 70% to 80%, 80% to 90%, or 90 to 99% sequence identity with a wild type STING nucleic acid sequence. In some embodiments, the nucleic acid encoding STING is a nucleic acid with 40% or more, 45% or more, 50% or more, 55% or more, 60% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more or 99% or more sequence identity with a wild type STING nucleic acid sequence.
Amino acid sequences of STING include, but are not limited to, those described in: Nitta et al. Hepatology 57(1): 46-58 (2013) and Jin et al. J. Immunol. 190(6): 2835-2843 (2013) and those deposited in GENBANK and assigned deposit numbers: NM_—198282.2 and NP_—938023.1 (human); NM_—028261.1 and NP_—082537.1 (mus musculus); and NM_—057386.4 and NP_—476734.1 (Drosophila melanogaster).
In certain embodiments, the STING polypeptide has the following sequence:

(SEQ ID NO: 05)

MPHSSLHPSIPCPRGHGAQKAALVLLSACLVTLWGLGEPPEHTLRYLVL

HLASLQLGLLLNGVCSLAEELRHIHSRYRGSYWRTVRACLGCPLRRGAL

LLLSIYFYYSLPNAVGPPFTWMLALLGLSQALNILLGLKGLAPAEISAV

CEKGNFNVAHGLAWSYYIGYLRLILPELQARIRTYNQHYNNLLRGAVSQ

RLYILLPLDCGVPDNLSMADPNIRFLDKLPQQTGDHAGIKDRVYSNSIY

ELLENGQRAGTCVLEYATPLQTLFAMSQYSQAGFSREDRLEQAKLFCRT

LEDILADAPESQNNCRLIAYQEPADDSSFSLSQEVLRHLRQEEKEEVTV

GSLKTSAVPSTSTMSQEPELLISGMEKPLPLRTDFS.

In other embodiments, the STING polypeptide has the following sequence:

(SEQ ID NO: 06)

MPHSSLHPSIPCPRGHGAQKAALVLLSACLVTLWGLGEPPEHTLRYLVL

HLASLQLGLLLNGVCSLAEELHHIHSRYRGSYWRTVRACLGCPLRRGAL

LLLSIYFYYSLPNAVGPPFTWMLALLGLSQALNILLGLKGLAPAEISAV

CEKGNFNVAHGLAWSYYIGYLRLILPELQARIRTYNQHYNNLLRGAVSQ

RLYILLPLDCGVPDNLSMADPNIRFLDKLPQQTADRAGIKDRVYSNSIY

ELLENGQRAGTCVLEYATPLQTLFAMSQYSQAGFSREDRLEQAKLFCQT

LEDILADAPESQNNCRLIAYQEPADDSSFSLSQEVLRHLRQEEKEEVTV

GSLKTSAVPSTSTMSQEPELLISGMEKPLPLRTDFS.

In some embodiments, the STING polypeptide is a polypeptide that has 40% to 99%, 45% to 99%, 50% to 99%, 55% to 99%, 60% to 99%, 65% to 99%, 70% to 99%, 75% to 99%, 80% to 99%, 85% to 99%, 90% to 99% or, 95% to 99% sequence identity with a wild type STING amino acid sequence. In some embodiments, the cGAS polypeptide is a polypeptide that has 40% to 50%, 50% to 60%, 60% to 70%, 70% to 80%, 80% to 90%, or 90 to 99% sequence identity with a wild type STING amino acid sequence. In some embodiments, the STING polypeptide is a polypeptide that has 40% or more, 45% or more, 50% or more, 55% or more, 60% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more or 99% or more sequence identity with a wild type STING amino acid sequence.
The above methods find use in a variety of different applications. Certain applications are now reviewed in the following Utility section.

Utility

The methods and compositions provided herein find use in a variety of applications, where such applications include increasing type I interferon (e.g., interferon-β) in a subject is desired. In addition, the methods and compositions provided herein find use in a variety of applications, where such applications include increasing STING mediated response in a subject is desired. Specific applications of interest include those in which a subject is treated for a disease condition that would benefit from an increase in type I interferon by providing the subject with a therapeutically effective amount of a cyclic-di-nucleotide active agent. In some instances, it may be desirable to increase a type I interferon or STING mediated response in a healthy individual, e.g., for the prevention of a disease or condition. As such, in some embodiments, the methods and compositions provided herein can be used to produce an ‘adjuvant’ effect in a vaccine to prevent an infection or other disease, wherein the active agent stimulates immunological memory to protect against future disease or infection.
In some embodiments, subjects suitable for treatment with a method described herein include individuals having an immunological or inflammatory disease or disorder including, but not limited to a cancer, an autoimmune disease or disorder, an allergic reaction, a chronic infectious disease and an immunodeficiency disease or disorder.
In some embodiments, subjects suitable for treatment with a method of the present invention include individuals having a cellular proliferative disease, such as a neoplastic disease (e.g., cancer). Cellular proliferative disease is characterized by the undesired propagation of cells, including, but not limited to, neoplastic disease conditions, e.g., cancer.
Examples of cellular proliferative disease include, but not limited to, abnormal stimulation of endothelial cells (e.g., atherosclerosis), solid tumors and tumor metastasis, benign tumors, for example, hemangiomas, acoustic neuromas, neurofibromas, trachomas, and pyogenic granulomas, vascular malfunctions, abnormal wound healing, inflammatory and immune disorders, Bechet's disease, gout or gouty arthritis, abnormal angiogenesis accompanying, for example, rheumatoid arthritis, psoriasis, diabetic retinopathy, other ocular angiogenic diseases such as retinopathy of prematurity (retrolental fibroplastic), macular degeneration, corneal graft rejection, neurovascular glaucoma and Oster Webber syndrome, psoriasis, restenosis, fungal, parasitic and viral infections such cytomegaloviral infections. Subjects to be treated according to the methods of the invention include any individual having any of the above-mentioned disorders.
In other embodiments, subjects suitable for treatment with a subject method include individuals who have been clinically diagnosed as infected with a virus. In some embodiments, the virus is a hepatitis virus (e.g., HAV, HBV, HCV, delta, etc.), particularly HCV, are suitable for treatment with the methods of the instant invention. Individuals who are infected with HCV are identified as having HCV RNA in their blood, and/or having anti-HCV antibody in their serum. Such individuals include naïve individuals (e.g., individuals not previously treated for HCV, particularly those who have not previously received IFN-α-based or ribavirin-based therapy) and individuals who have failed prior treatment for HCV.
In some embodiments, subjects suitable for treatment with a method provided herein include an individual with a neurodegenerative disease or disorder, including, but not limited to, Parkinson's disease, Alzheimer's disease, Huntington's disease, and Amyotrophic lateral sclerosis (ALS).
In other embodiments, subjects suitable for treatment with a method of the present invention include individuals having multiple sclerosis. Multiple sclerosis refers to an autoimmune neurodegenerative disease, which is marked by inflammation within the central nervous system with lymphocyte attack against myelin produced by oligodendrocytes, plaque formation and demyelization with destruction of the myelin sheath of axons in the brain and spinal cord, leading to significant neurological disability over time. Typically, at onset an otherwise healthy person presents with the acute or sub acute onset of neurological symptomatology (attack) manifested by unilateral loss of vision, vertigo, ataxia, dyscoordination, gait difficulties, sensory impairment characterized by paresthesia, dysesthesia, sensory loss, urinary disturbances until incontinence, diplopia, dysarthria or various degrees of motor weakness until paralysis. The symptoms may be painless, remain for several days to a few weeks, and then partially or completely resolve. After a period of remission, a second attack will occur. During this period after the first attack, the patient is defined to suffer from probable MS. Probable MS patients may remain undiagnosed for years. When the second attack occurs the diagnosis of clinically definite MS (CDMS) is made (Poser criteria 1983; C. M. Poser et al., Ann. Neurol. 1983; 13, 227).
The terms “subject” and “patient” mean a member or members of any mammalian or non-mammalian species that may have a need for the pharmaceutical methods, compositions and treatments described herein. Subjects and patients thus include, without limitation, primate (including humans), canine, feline, ungulate (e.g., equine, bovine, swine (e.g., pig)), avian, and other subjects. Humans and non-human animals having commercial importance (e.g., livestock and domesticated animals) are of particular interest.
“Mammal” means a member or members of any mammalian species, and includes, by way of example, canines; felines; equines; bovines; ovines; rodentia, etc. and primates, particularly humans. Non-human animal models, particularly mammals, e.g., primate, murine, lagomorpha, etc. may be used for experimental investigations.
“Treating” or “treatment” of a condition or disease includes: (1) preventing at least one symptom of the conditions, i.e., causing a clinical symptom to not significantly develop in a mammal that may be exposed to or predisposed to the disease but does not yet experience or display symptoms of the disease, (2) inhibiting the disease, i.e., arresting or reducing the development of the disease or its symptoms, or (3) relieving the disease, i.e., causing regression of the disease or its clinical symptoms. As used herein, the term “treating” is thus used to refer to both prevention of disease, and treatment of pre-existing conditions. For example, where the cyclic-di-nucleotide active agent is administered, the prevention of cellular proliferation can be accomplished by administration of the subject compounds prior to development of overt disease, e.g., to prevent the regrowth of tumors, prevent metastatic growth, etc. Alternatively the compounds are used to treat ongoing disease, by stabilizing or improving the clinical symptoms of the patient.

Combination Therapy

For use in the subject methods, the cyclic-di-nucleotide active agent described herein may be administered in combination with other pharmaceutically active agents, including other agents that treat the underlying condition or a symptom of the condition. “In combination with” as used herein refers to uses where, for example, the first compound is administered during the entire course of administration of the second compound; where the first compound is administered for a period of time that is overlapping with the administration of the second compound, e.g., where administration of the first compound begins before the administration of the second compound and the administration of the first compound ends before the administration of the second compound ends; where the administration of the second compound begins before the administration of the first compound and the administration of the second compound ends before the administration of the first compound ends; where the administration of the first compound begins before administration of the second compound begins and the administration of the second compound ends before the administration of the first compound ends; where the administration of the second compound begins before administration of the first compound begins and the administration of the first compound ends before the administration of the second compound ends. As such, “in combination” can also refer to regimen involving administration of two or more compounds. “In combination with” as used herein also refers to administration of two or more compounds that may be administered in the same or different formulations, by the same of different routes, and in the same or different dosage form type.
Examples of other agents for use in combination therapy of neoplastic disease include, but are not limited to, thalidomide, marimastat, COL-3, BMS-275291, squalamine, 2-ME, SU6668, neovastat, Medi-522, EMD121974, CAI, celecoxib, interleukin-12, IM862, TNP470, avastin, gleevec, herceptin, and mixtures thereof. Examples of chemotherapeutic agents for use in combination therapy include, but are not limited to, daunorubicin, daunomycin, dactinomycin, doxorubicin, epirubicin, idarubicin, esorubicin, bleomycin, mafosfamide, ifosfamide, cytosine arabinoside, bis-chloroethylnitrosurea, busulfan, mitomycin C, actinomycin D, mithramycin, prednisone, hydroxyprogesterone, testosterone, tamoxifen, dacarbazine, procarbazine, hexamethylmelamine, pentamethylmelamine, mitoxantrone, amsacrine, chlorambucil, methylcyclohexylnitrosurea, nitrogen mustards, melphalan, cyclophosphamide, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-azacytidine, hydroxyurea, deoxycoformycin, 4-hydroxyperoxycyclophosphor-amide, 5-fluorouracil (5-FU), 5-fluorodeoxyuridine (5-FUdR), methotrexate (MTX), colchicine, taxol, vincristine, vinblastine, etoposide (VP-16), trimetrexate, irinotecan, topotecan, gemcitabine, teniposide, cisplatin and diethylstilbestrol (DES).
Other antiviral agents can also be delivered in the treatment methods of the invention. For example, compounds that inhibit inosine monophosphate dehydrogenase (IMPDH) may have the potential to exert direct anti viral activity, and such compounds can be administered in combination with the mutant Listeria, as described herein. Drugs that are effective inhibitors of hepatitis C NS3 protease may be administered in combination with the mutant Listeria, as described herein. Hepatitis C NS3 protease inhibitors inhibit viral replication. Other agents such as inhibitors of HCV NS3 helicase are also attractive drugs for combinational therapy, and are contemplated for use in combination therapies described herein. Ribozymes such as Heptazyme™ and phosphorothioate oligonucleotides which are complementary to HCV protein sequences and which inhibit the expression of viral core proteins are also suitable for use in combination therapies described herein. Examples of other agents for use in combination therapy of multiple sclerosis include, but are not limited to; glatiramer; corticosteroids; muscle relaxants, such as Tizanidine (Zanaflex) and baclofen (Lioresal); medications to reduce fatigue, such as amantadine (Symmetrel) or modafinil (Provigil); and other medications that may also be used for depression, pain and bladder or bowel control problems that can be associated with MS.
In the context of a combination therapy, combination therapy compounds may be administered by the same route of administration (e.g., intrapulmonary, oral, enteral, etc.) that the cyclic-di-nucleotide active agents are administered. In the alternative, the compounds for use in combination therapy with the cyclic-di-nucleotide active agent may be administered by a different route of administration.

Adjuvants

In certain embodiments, the cyclic di-nucleotide active agent functions as an adjuvant when administered together with a drug or vaccine to treat or prevent a disease or condition, including, but not limited to, those diseases and conditions provided herein. In some embodiments, the cyclic di-nucleotide active agents are administered together with a vaccine. Such active agents that are administered with a vaccine can function as an adjuvant to enhance the immune response elicited by the vaccine, including stimulating immunological memory to protect against future diseases and/or infections.
In certain embodiments, the cyclic di-nucleotide or STING active agents administered as an adjuvant for a vaccine can enhance the effectiveness of the vaccine by, e.g., increasing the immunogenicity of weaker antigens, reducing the amount of antigen required to elicit a immune response, reducing the frequency of immunization necessary to maintain protective immunity, enhance the efficacy of vaccines in immunocompromised or other individuals with reduced immune responses, and/or increase immunity at a target tissue, such as mucosal immunity. In such embodiments, the cyclic di-nucleotide active agents, when co-administered with one or more antigens, can induce a particular cytokine profile to promote cellular and humoral immunity against the antigen and increase the effectiveness of vaccination.
Antigens used to prepare vaccines may be derived from a variety of microorganisms such as viruses, bacteria and parasites that contain substances that are not normally present in the body, as well as tumor cells. These substances can be used as antigens to produce an immune response to destroy both the antigen and cells containing the antigen, such as a bacterial cell or cancer cell. In certain instances, isolated or crude antigens of microbial pathogens can be used in vaccines to treat infectious disease; isolated or crude tumor cell antigens can be used in vaccines to treat cancer; isolated or crude antigens known to be associated with a pathologically aberrant cell can be used to treat a variety of diseases in which it is beneficial to target particular cells for destruction.
Microorganisms that may be a source of antigen include clinically relevant microorganisms, such as bacteria, including pathogenic bacteria; viruses (e.g., Influenza, Measles, Coronavirus); parasites (e.g., Trypanosome, Plasmodium, Leishmania); fungi (e.g., Aspergillus, Candida, Coccidioides, Cryptococcus); and the like. For example, the antigen may be from bacteria, particularly pathogenic bacteria, such as the causative agent of anthrax (Bacillus anthracis), plague (Yersinia pestis), tuberculosis (Mycobacterium tuberculosis), salmonellosis (Salmonella enterica), stomach cancer (Helicobacter pylori), sexually transmitted diseases (Chlamydia trachomatis or Neisseria gonorrhea), and the like. Other representative examples include antigens from certain viruses, such as influenza virus(es), Norwalk virus, smallpox virus, West Nile virus, SARS virus, MERS virus, respiratory syncytial virus, measles virus, and the like. Fungi of interest include, but are not limited to Candida albicans or Aspergillus spp., and parasites of interest include the causative agents of trypanosomiasis, leishmania, pneumonic plague, and lyme disease (Borrellia burgdorferi).
A pathologically aberrant cell to be used in a vaccine can be obtained from any source such as one or more individuals having a pathological condition or ex vivo or in vitro cultured cells obtained from one or more such individuals, including a specific individual to be treated with the resulting vaccine.
A vaccine formulation for use with an adjuvant containing cyclic di-nucleotide active agents may include, e.g., attenuated and inactivated viral and bacterial pathogens from infected patients or propagated cultures, purified macromolecules, polysaccharides, toxoids, recombinant antigens, organisms containing a foreign gene from a pathogen, synthetic peptides, polynucleic acids, antibodies and tumor cells.
Recombinant antigens may be obtained, for example, by isolating and cloning a gene encoding any immunogenic polypeptide, in, e.g., bacterial, yeast, insect, reptile or mammalian cells using recombinant methods well known in the art and described, for example in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York (1992) and in Ansubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1998). A number of genes encoding surface antigens from viral, bacterial and protozoan pathogens have been successfully cloned, expressed and used as antigens for vaccine development. For example, the major surface antigen of hepatitis B virus, HbsAg, the b subunit of choleratoxin, the enterotoxin of E. coli, the circumsporozoite protein of the malaria parasite, and a glycoprotein membrane antigen from Epstein-Barr virus, as well as tumor cell antigens, have been expressed in various well known vector/host systems, purified and used in vaccines.
A vaccine formulation containing cyclic di-nucleotide or STING active agents may advantageously contain other vaccine adjuvants and carriers. These carriers and adjuvants include, but are not limited to, ion exchange resins, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, phosphate buffered saline solution, water, emulsions (e.g. oil/water emulsion), salts or electrolytes such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances and polyethylene glycol.
Any convenient method for determining if a vaccine compound or formulation induces an innate, humoral, cell-mediated, or any combination of these types of immune response may be employed. For example, the ability of a vaccine compound or formulation to induce an innate immune response through STING can be determined using methods described herein as well as other methods. Such methods for detecting an innate immune response can be generally performed within hours of vaccine administration. The ability of a vaccine compound or formulation to induce a humoral response can be determined by measuring the titer of antigen-specific antibodies in an animal primed with the vaccine and boosted with the antigen, or determining the presence of antibodies cross-reactive with an antigen by ELISA, Western blotting or other well-known methods. Cellular immune responses can be determined, for example, by measuring cytotoxic T cell response to antigen using a variety of methods, such as, e.g., FACS sorting, and other methods well known in the art. Methods of detecting humoral and cellular immune responses can be generally performed days or weeks after vaccine administration.

Cyclic-Di-Nucleotides

In another aspect, provided herein are 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides. As used herein, “cyclic-di-nucleotide” refers to a compound containing two nucleosides (i.e., a first and second nucleoside), wherein the 2′ or 3′ carbon of each nucleoside is linked to the 5′ carbon of the other nucleoside by a phosphodiester bond. Therefore, a 2′-5′ phosphodiester linkage containing cyclic-di-nucleotide refers to a cyclic-di-nucleotide, wherein the 2′ carbon of at least one of the nucleosides is linked to the 5′ carbon of the other nucleoside. As discussed herein, 2′-5′ phosphodiester linkage containing cyclic-di-nucleotides can be used in practicing the methods described herein for increasing production of a type I interferon in a cell or subject. As used herein a “cyclic-di-nucleotide” also includes all of the stereoisomeric forms of the cyclic-di-nucleotides described herein.
As used herein, a “nucleoside” refers to a composition containing a nitrogenous base covalently attached to a sugar (e.g., ribose or deoxyribose) or an analog thereof. Examples of nucleosides include, but are not limited to cytidine, uridine, adenosine, guanosine, thymidine and inosine. In some embodiments, the nucleoside contains a deoxyribose sugar. Analogs of nucleosides include, but are not limited to dexoyadenosine analogues (e.g., Didanosine and Vidarabine); deoxycytidine analogues (e.g., Cytarabine, Ematricitabine, Lamivudine, and Zalcitabine); deoxyguanosine analogues (Abacavir and Entecavir); (deoxy-) thymidine analogues (e.g., Stavudine, Telbivudine, and Zidovudine); and deoxyuridine alaogues (e.g., Idoxuridine and Trifluridine).
While not being bound by any particular theory of operation, and as shown in the examples below, cyclic-di-nucleotides can increase type-I IFN production in a cell. In certain embodiments, cyclic-di-nucleotides increase type-I IFN production through a mechanism that involves stimulator of interferon genes (STING).
Cyclic-di-nucleotides include those specifically described herein as well as isoforms (e.g., tautomers) of those specifically described herein that can be used in practicing the subject methods. Cyclic-di-nucleotides can be obtained using any suitable method. For example, cyclic-di-nucleotides may be made by chemical synthesis using nucleoside derivatives as starting material. Cyclic-di-nucleotides can also be produced by in vitro synthesis, using recombinant purified cGAMP synthase (cGAS), as described in the Experimental Section below. Moreover, the structures of such cyclic-di-nucleotides can be confirmed using NMR analysis.
Cyclic-di-nucleotides provided herein can be described by the following nomenclature: cyclic[X₁(A-5′)pX₂(B-5′)p], wherein X₁and X₂are the first and second nucleoside, A is the carbon of the first nucleoside (e.g., 2′ or 3′ position) that is linked to the 5′ carbon of the second nucleoside via a phosphodiester bond and B is the carbon of the second nucleoside (e.g., 2′ or 3′ position) that is linked to the 5′ carbon of the first nucleoside by a phosphodiester bond. For instance, based on this nomenclature, cyclic[G(2′-5′)pA(3′-5′)p] has the following formula:
In certain embodiments, the cyclic-di-nucleotide contains a 2′-5′ phosphodiester bond. In particular embodiments, the cyclic-di-nucleotide further contains a 3′-5′ phosphodiester bond (e.g., cyclic[X₁(2′-5′)pX₂(3′-5′)p] or cyclic[X₁(3′-5′)pX₂(2′-5′)p]). In other embodiments, the cyclic-di-nucleotide contains two 2′-5′ phosphodiester bonds (cyclic[X₁(2′-5′)pX₂(2′-5′)p]).
In certain embodiments, the cyclic-di-nucleotide is:
cyclic[A(2′-5′)pA2′-5′)p];
cyclic[T(2′-5′)pT(2′-5′)p];
cyclic[G(2′-5′)pG(2′-5′)p];
cyclic[C(2′-5′)pC(2′-5′)p]; or
cyclic[U(2′-5′)pU(2′-5′)p].
In certain embodiments, the cyclic-di-nucleotide is:
cyclic[A(2′-5′)pA(3′-5′)p];
cyclic[T(2′-5′)pT(3′-5′)p];
cyclic[G(2′-5′)pG(3′-5′)p];
cyclic[C(2′-5′)pC(3′-5′)p];
cyclic[U(2′-5′)pU(3′-5′)p];
cyclic[A(2′-5′)pT(3′-5′)p];
cyclic[T(2′-5′)pA(3′-5′)p];
cyclic[A(2′-5′)pG(3′-5′)p];
cyclic[G(2′-5′)pA(3′-5′)p];
cyclic[A(2′-5′)pC (3′-5′)p];
cyclic[C(2′-5′)pA(3′-5′)p];
cyclic[A(2′-5′)pU(3′-5′)p];
cyclic[U(2′-5′)pA(3′-5′)p];
cyclic[T(2′-5′)pG(3′-5′)p];
cyclic[G(2′-5′)pT(3′-5′)p];
cyclic[T2′-5′)pC(3′-5′)p];
cyclic[C(2′-5′)pT(3′-5′)p];
cyclic[T(2′-5′)pU(3′-5′)p];
cyclic[U(2′-5′)pT(3′-5′)p];
cyclic[G(2′-5′)pC(3′-5′)p];
cyclic[C2′-5′)pG(3′-5′)p];
cyclic[G(2′-5′)pU(3′-5′)p];
cyclic[U(2′-5′)pG(3′-5′)p];
cyclic[C(2′-5′)pU(3′-5′)p]; or
cyclic[U(2′-5′)pC(3′-5′)p].
In certain embodiments, the cyclic-di-nucleotide has the following formula:
wherein X and Y can be any organic molecule including a nitrogenous base. As used herein a “nitrogenous base” refers to nitrogen-containing molecules having the chemical properties of a base including, but not limited to, pyrimidine derivatives (e.g., cytosine, thymine, and uracil) and purine derivatives (e.g., adenine and guanine), as well as substituted pyrimidine and purine derivatives, pyrimidine and purine analogs, and their tautomers. In certain embodiments, X and Y are each one of the following:
In certain embodiments, the cyclic-di-nucleotide has the following formula (cyclic[G(2′5′)pA(3′5′)p]):
In certain embodiments, the cyclic-di-nucleotide has the following formula (cyclic[G(3′5′)pA(2′5′)p]):
In other embodiments, the cyclic-di-nucleotide has the following formula cyclic[G(2′5′)pA(2′5′)p]:
In other embodiments, the cyclic-di-nucleotide has the following formula cyclic[A(2′5′)pA(3′5′)p]:
In yet other embodiments, the cyclic-di-nucleotide has the following formula cyclic[G(2′5′)pG(3′5′)p]:
In certain embodiments, the cyclic-di-nucleotide has the following formula cyclic[A(2′5′)pA(2′5′)p]:
In certain embodiments, the cyclic-di-nucleotide has the following formula cyclic[G(2′5′)pG(2′5′)p]:
In certain embodiments, the cyclic-di-nucleotide has one of the following formulas:
wherein R is any amino acid side chain.

Pharmaceutical Compositions

In another aspect, provided herein is a pharmaceutical composition that contains any of the cyclic-di-nucleotide active agents provided herein and a pharmaceutically acceptable carrier. In certain embodiments of the pharmaceutical composition, the cyclic-di-nucleotide active agent is one or more cyclic-di-nucleotides.
The term “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized foreign pharmacopeia for use in animals, and more particularly in humans. The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the mitochondrial transport protein inhibitor is administered. Such pharmaceutical carriers can be, for example, sterile liquids, such as saline solutions in water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. A saline solution is a preferred carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene glycol, water, ethanol and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. The inhibitors can be formulated as neutral or salt forms. Pharmaceutically acceptable salts include those formed with free amino groups such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with free carboxyl groups such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc. Examples of suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin, hereby incorporated by reference herein in its entirety. Such compositions will contain a therapeutically effective amount of the mitochondrial transport protein (e.g., a Miro protein, a TRAK protein, or Khc) inhibitor, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient. The formulation should suit the mode of administration.
The pharmaceutical composition can also include any of a variety of stabilizing agents, such as an antioxidant for example. When the pharmaceutical composition includes a polypeptide, the polypeptide can be complexed with various well-known compounds that enhance the in vivo stability of the polypeptide, or otherwise enhance its pharmacological properties (e.g., increase the half-life of the polypeptide, reduce its toxicity, enhance solubility or uptake). Examples of such modifications or complexing agents include sulfate, gluconate, citrate and phosphate. The polypeptides of a composition can also be complexed with molecules that enhance their in vivo attributes. Such molecules include, for example, carbohydrates, polyamines, amino acids, other peptides, ions (e.g., sodium, potassium, calcium, magnesium, manganese), and lipids.
Further guidance regarding formulations that are suitable for various types of administration can be found in Remington's Pharmaceutical Sciences, Mace Publishing Company, Philadelphia, Pa., 17th ed. (1985). For a brief review of methods for drug delivery, see, Langer, Science 249:1527-1533 (1990).
The components used to formulate the pharmaceutical compositions are preferably of high purity and are substantially free of potentially harmful contaminants (e.g., at least National Food (NF) grade, generally at least analytical grade, and more typically at least pharmaceutical grade). Moreover, compositions intended for in vivo use may be sterile. To the extent that a given compound must be synthesized prior to use, the resulting product is typically substantially free of any potentially toxic agents, particularly any endotoxins, which may be present during the synthesis or purification process. Compositions for parental administration are also sterile, substantially isotonic and made under GMP conditions.
The pharmaceutical composition can be formulated for intravenous, oral, via implant, transmucosal, transdermal, intramuscular, intrathecal, or subcutaneous administration. In some embodiments, the pharmaceutical composition is formulated for intravenous administration. In other embodiments, the pharmaceutical composition is formulated for subcutaneous administration. The following delivery systems, which employ a number of routinely used pharmaceutical carriers, are only representative of the many embodiments envisioned for administering the instant compositions.
Injectable drug delivery systems include solutions, suspensions, gels, microspheres and polymeric injectables, and can comprise excipients such as solubility-altering agents (e.g., ethanol, propylene glycol and sucrose) and polymers (e.g., polycaprylactones and PLGAs). Implantable systems include rods and discs, and can contain excipients such as PLGA and polycaprylactone. Osteopontin or nucleic acids of the invention can also be administered attached to particles using a gene gun.
Oral delivery systems include tablets and capsules. These can contain excipients such as binders (e.g., hydroxypropylmethylcellulose, polyvinyl pyrilodone, other cellulosic materials and starch), diluents (e.g., lactose and other sugars, starch, dicalcium phosphate and cellulosic materials), disintegrating agents (e.g., starch polymers and cellulosic materials) and lubricating agents (e.g., stearates and talc).
Transmucosal delivery systems include patches, tablets, suppositories, pessaries, gels and creams, and can contain excipients such as solubilizers and enhancers (e.g., propylene glycol, bile salts and amino acids), and other vehicles (e.g., polyethylene glycol, fatty acid esters and derivatives, and hydrophilic polymers such as hydroxypropylmethylcellulose and hyaluronic acid).
Dermal delivery systems include, for example, aqueous and nonaqueous gels, creams, multiple emulsions, microemulsions, liposomes, ointments, aqueous and nonaqueous solutions, lotions, aerosols, hydrocarbon bases and powders, and can contain excipients such as solubilizers, permeation enhancers (e.g., fatty acids, fatty acid esters, fatty alcohols and amino acids), and hydrophilic polymers (e.g., polycarbophil and polyvinylpyrolidone). In one embodiment, the pharmaceutically acceptable carrier is a liposome or a transdermal enhancer.
In certain embodiments, the pharmaceutical composition containing the cyclic-di-nucleotide active agent is formulated to cross the blood brain barrier (BBB). One strategy for drug delivery through the blood brain barrier (BBB) entails disruption of the BBB, either by osmotic means such as mannitol or leukotrienes, or biochemically by the use of vasoactive substances such as bradykinin. A BBB disrupting agent can be co-administered with the therapeutic compositions when the compositions are administered by intravascular injection. Other strategies to go through the BBB may entail the use of endogenous transport systems, including caveoil-1 mediated transcytosis, carrier-mediated transporters such as glucose and amino acid carriers, receptor-mediated transcytosis for insulin or transferrin, and active efflux transporters such as p-glycoprotein. Active transport moieties may also be conjugated to the therapeutic compounds for use in the invention to facilitate transport across the endothelial wall of the blood vessel. Alternatively, drug delivery of the ND pharmaceutical composition behind the BBB may be by local delivery, for example by intrathecal delivery, e.g., through an Ommaya reservoir (see, e.g., U.S. Pat. Nos. 5,222,982 and 5,385,582, incorporated herein by reference); by bolus injection, e.g., by a syringe, e.g., intravitreally or intracranially; by continuous infusion, e.g., by cannulation, e.g., with convection (see, e.g., US Application No. 20070254842, incorporated here by reference); or by implanting a device upon which the inhibitor pharmaceutical composition has been reversably affixed (see e.g., US Application Nos. 20080081064 and 20090196903, incorporated herein by reference).
In certain embodiments, the pharmaceutical composition containing the cyclic-di-nucleotide or STING active agents is formulated in a delivery vehicle, e.g., to enhance cytosolic transport. Any convenient protocol may be employed to facilitate delivery of the cyclic-di-nucleotide active agent across the plasma membrane of a cell and into the cytosol. In certain embodiments, the cyclic-di-nucleotide or STING active agents and an antigen effective for use in a vaccine may be formulated together to be delivered by the same delivery vehicle in the pharmaceutical composition.
In some instances, the cyclic-di-nucleotide or STING active agents may be encapsulated in a delivery vehicle comprising liposomes in the pharmaceutical composition. Methods of using liposomes for drug delivery and other therapeutic uses are known in the art. See, e.g., U.S. Pat. No. 8,329,213, U.S. Pat. No. 6,465,008, U.S. Pat. No. 5,013,556, US Application No. 20070110798, and Andrews et al., Mol Pharm 2012 9:1118, which are incorporated herein by reference. Liposomes may be modified to render their surface more hydrophilic by adding polyethylene glycol (“pegylated”) to the bilayer, which increases their circulation time in the bloodstream. These are known as “stealth” liposomes and are especially useful as carriers for hydrophilic (water soluble) molecules, such as the cyclic-di-nucleotide active agents.
In certain embodiments, nano- or microparticles made from biodegradable materials such as poly(lactic acid), poly(γ-glutamic acid), poly(glycolic acid), polylactic-co-glycolic acid. Polyethylenimine, or alginate microparticles, and cationic microparticles, including dedrimers, such as cyclodextrins, may be employed as delivery vehicles for cyclic-di-nucleotide or STING active agents to promote cellular uptake. See, e.g., U.S. Pat. No. 8,187,571, Krishnamachari et al., Adv Drug Deliv Rev 2009 61:205, Garzon et al., 2005 Vaccine 23:1384, incorporated herein by reference.
In another embodiment, photochemical internalization may be employed to enhance cytosolic uptake of cyclic-di-nucleotide or STING active agents. See, e.g., US Application No. 20120226217, incorporated herein by reference. In such embodiments, the cyclic-di-nucleotide or STING active agents may be co-adiminstered with a photosensitizing agent. Then, exposure of the target cells to light of a specific wavelength triggers internalization of the cyclic-di-nucleotide or STING active agents.
In certain embodiments, the delivery vehicle for delivering the cyclic-di-nucleotide or STING active agents can also be targeting delivery vehicles, e.g., a liposome containing one or more targeting moieties or biodistribution modifiers on the surface of the liposome. A targeting moiety can be any agent that is capable of specifically binding or interacting with a desired target.
The specific binding agent can be any molecule that specifically binds to a protein, peptide, biomacromolecule, cell, tissue, etc. that is being targeted (e.g., a protein peptide, biomacromolecule, cell, tissue, etc. wherein the cyclic-di-nucleotide or STING active agent exerts its desired effect). Depending on the nature of the target site, the specific binding agent can be, but is not limited to, an antibody against an epitope of a peptidic analyte, or any recognition molecule, such as a member of a specific binding pair. For example, suitable specific binding pairs include, but are not limited to: a member of a receptor/ligand pair; a ligand-binding portion of a receptor; a member of an antibody/antigen pair; an antigen-binding fragment of an antibody; a hapten; a member of a lectin/carbohydrate pair; a member of an enzyme/substrate pair; biotin/avidin; biotin/streptavidin; digoxin/antidigoxin; a member of a peptide aptamer binding pair; and the like.
In certain embodiments, the specific binding moiety includes an antibody. An antibody as defined here may include fragments of antibodies which retain specific binding to antigen, including, but not limited to, Fab, Fv, scFv, and Fd fragments, chimeric antibodies, humanized antibodies, single-chain antibodies, and fusion proteins comprising an antigen-binding portion of an antibody and a non-antibody protein. The antibodies may also include Fab′, Fv, F(ab′)₂, and or other antibody fragments that retain specific binding to antigen.
In certain embodiments, the targeting moiety is a binding agent that specifically interacts with a molecule expressed on a tumor cell or an immune cell (e.g., CD4, CD8, CD69, CD62L, and the like), such that the targeting delivery vehicle containing the cyclic-di-nucleotide or STING active agents is delivered to the site of a tumor or to specific immune cells.
Where desired, any combinations of the above listed delivery vehicles may be used advantageously to enhance delivery of the cyclic-di-nucleotide or STING active agents to the target cells.
Components of the pharmaceutical composition can be supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the composition is administered by injection, an ample of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.
In some embodiments, the pharmaceutical composition is supplied as a dry sterilized lyophilized powder that is capable of being reconstituted to the appropriate concentration for administration to a subject. In some embodiments, the pharmaceutical composition is supplied as a water free concentrate. In some embodiments, the pharmaceutical composition is supplied as a dry sterile lyophilized powder at a unit dosage of at least 0.5 mg, at least 1 mg, at least 2 mg, at least 3 mg, at least 5 mg, at least 10 mg, at least 15 mg, at least 25 mg, at least 30 mg, at least 35 mg, at least 45 mg, at least 50 mg, at least 60 mg, or at least 75 mg.
Solutions, suspensions and powders for reconstitutable delivery systems include vehicles such as suspending agents (e.g., gums, xanthans, cellulosics and sugars), humectants (e.g., sorbitol), solubilizers (e.g., ethanol, water, PEG and propylene glycol), surfactants (e.g., sodium lauryl sulfate, Spans, Tweens, and cetyl pyridine), preservatives and antioxidants (e.g., parabens, vitamins E and C, and ascorbic acid), anti-caking agents, coating agents, and chelating agents (e.g., EDTA).
In some embodiments, the pharmaceutical composition is formulated as a salt form. Pharmaceutically acceptable salts include those formed with anions such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with cations such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.
In certain embodiments, the pharmaceutical composition contains a prodrug derivative of any of the cyclic-di-nucleotide or STING active agents provided herein. Such prodrugs can be subsequently converted to an active form of the cyclic-di-nucleotide or STING active agent in the body of the subject administered the pharmaceutical composition.

Kits

Kits with unit doses of the subject cyclic-di-nucleotide active agents, e.g., one or more cyclic-di-nucleotides, e.g., in oral or injectable doses, are provided. In the subject kits, the one or more components are present in the same or different containers, as may be convenient or desirable.
In addition to the containers containing the unit doses will be instructions describing the use and attendant benefits of the cyclic-di-nucleotide in treating a pathological condition of interest. Instructions may be provided in a variety of different formats. In certain embodiments, the instructions may include complete protocols for practicing the subject methods or means for obtaining the same (e.g., a website URL directing the user to a webpage which provides the instructions), where these instructions may be printed on a substrate, where substrate may be one or more of: a package insert, the packaging, reagent containers and the like.
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.

EXPERIMENTAL

I. Results and Discussion

Recognition of pathogen-derived nucleic acid is a major mechanism by which innate immune responses are initiated in mammals (Barbalat et al., Annu Rev Immunol (2011) 29: 185). Several families of germ-line encoded nucleic acid sensors have been described, including the Toll-like receptors (TLRs) and RIG-1-like receptors (RLRs)(Palm et al., Immunol Rev (2009) 227: 221; Takeuchi et al., Cell (2010) 140: 805). Upon binding nucleic acids, these sensors initiate signaling cascades that lead to the production of cytokines and other immune effector proteins that provide host defense.
The cytosolic presence of foreign double-stranded (ds) DNA triggers a potent antiviral response dominated by the production of type I interferons (IFNs) (Ishii et al., Nat. Immunol. (2006) 7: 40; Stetson et al., Immunity (2006) 24: 93). However, the molecular mechanism linking dsDNA to interferon production has not been well characterized (Burdette & Vance, Nat. Immunol. (2013) 14: 19). A host protein, STING, was identified and shown to be required for the IFN response to cytosolic dsDNA (Ishikawa & Barber, Nature (2008) 455: 674; Ishikawa et al., Nature (2009) 461: 788; Sun et al., Proc Natl Acad Sci USA (2009) 106: 8653; and Zhong et al., Immunity (2008) 29: 538). STING was also shown to be required for the interferon response to bacterially-derived second messengers called cyclic-di-nucleotides (CDNs)(Jin et al., J Immunol (2011) 187: 2595; and Sauer et al., Infect Immun (2011) 79: 688). CDNs are secreted or released into the cytosol by certain bacterial pathogens (Woodward et al., Science (2010) 328: 1703) and bind directly to STING (Burdette et al., Nature (2011) 478: 515). Interestingly, however, a mutant (R231A) allele of mouse STING was identified that abolished responsiveness to CDNs but did not appreciably affect the interferon response to cytosolic DNA (Id). In contrast, 293T cells expressing wild-type mouse STING are responsive to CDNs but not to dsDNA. Thus, although the IFN responses to cytosolic CDNs and dsDNA both require STING, the responses to these chemically distinct ligands can be genetically uncoupled.
Based on two studies (Sun, et al., Science (2013) 339: 786; and Wu et al., Science (2013) 339: 826), it was proposed that the cytosolic presence of dsDNA leads to the production of a CDN, cyclic-GMP-AMP (cGAMP), by a DNA-dependent sensor called cGAMP synthase (cGAS). cGAMP was shown to bind and activate STING. However, it remained unclear how the STING R231A mutant could still initiate responses to dsDNA despite lacking responsiveness to CDNs. Therefore, the mechanism by which cGAS activates STING was investigated.
Previous studies (Sauer et al., Burdette et al.) focused primarily on mouse STING and it was not yet clear whether human STING could respond to CDNs (Conlon et al., J Immunol, (2013) 190: 5216). As previously reported (Sun et al., Wu et al.) it was found that the human THP-1 cell line responded robustly to CDNs in a manner dependent on STING (FIG. 1A, B). hSTING was cloned from THP-1 cells and compared its amino acid sequence to the previously widely studied reference allele (NP_—938023.1; denoted here as hSTING^REF) (7) (FIG. 2). It was found that hSTING^REFand hSTING^THP-1differ at four amino acid positions. Notably, hSTING^REFencodes a histidine (H) at amino acid position 232, whereas hSTING^THP-1encodes an arginine (R) at this position, which corresponds to R231 in mSTING that is critical for responsiveness to CDNs. Therefore, the functionality of individual hSTING alleles were tested by expressing these alleles in 293T cells that lack endogenous STING (Burdette et al.). As previously observed (Burdette et al.), overexpression of mSTING in 293T cells is sufficient to induce ligand-independent activation of an IFN-luciferase reporter construct; however, transfection of 293T cells with lower amounts of mSTING renders the cells responsive to CDNs. Likewise, 293T cells expressing hSTING^THP-1were responsive to CDN stimulation. In contrast, cells expressing hSTING^REFwere poorly or non-responsive (FIG. 1C). Interestingly, it was observed that three recent crystal structures of STING bound to cyclic-di-GMP were of the poorly-responsive hSTING^REFprotein (Huang, et al., Nature Struct. & Mol. Biol. (2012) 19: 728; Ouyang et al., Immunity (2012) 36: 1073; Yin et al., Mol Cell (2012) 46: 735).
293T cells are not responsive to stimulation by dsDNA, presumably due to lack of expression of cGAS (Sun et al.) or perhaps other DNA sensors. Therefore, to test whether the hSTING variants could respond to DNA stimulation, STING-null (‘goldenticket’)(Sauer et al.), but (cGAS⁺) macrophages were transduced with hSTING expression vectors. Interestingly, even the hSTING^REFvariant that is non-responsive to CDNs conferred responsiveness to dsDNA (FIG. 1D). hSTING^REFtherefore phenocopies the R231A mutant of mouse STING, previously described that uncouples responsiveness to CDNs and dsDNA (Burdette et al.). Like the mSTING^R231Avariant, hSTING^REFstill bound to CDNs (FIG. 1E) (Huang et al., Ouyang et al., and Yin et al.), indicating that this allele is compromised at a step downstream of CDN binding.
Consistent with the above results with hSTING alleles, an R231H mutant of mSTING was poorly responsive to CDNs, as were R232A or R232H variants of hSTING^THP(FIG. 3A). It was therefore concluded that arginine 231/232 is critical for responsiveness to CDNs in mouse/human STING. Introduction of an H232R mutation in hSTING^REF, however was not sufficient to restore the responsiveness to CDNs; indeed, it was observed that a second substitution (G230A) was also required (FIG. 4). Again, all the variant STING alleles that were tested bound cyclic-di-GMP, consistent with the fact that residues 230 and 232 are located in loops that cover but do not form the CDN binding pocket (FIG. 3B) (Burdette & Vance).
Importantly, mSTING^R231Awas also non-responsive to chemically synthesized cGAMP (FIG. 1F) (Kellenberger, et al., J Am Chem. Soc. (2013). 135:4906). This raised the question of whether R231A/R232H variants of STING would be responsive to the cGAS enzyme that is believed to activate STING via production of cGAMP. It was found that human or mouse cGAS expression was sufficient to robustly activate hSTING^REFand mSTING^R231Avariants, even at very low levels of cGAS expression (FIG. 5A). Several explanations were considered for this result. One explanation is that the response is due simply to overexpression of the synthase in mammalian cells; however, overexpression of a bacterial enzyme that produces cGAMP (DncV from V. cholerae) (Davies, Cell (2012)149: 358) did not activate hSTING^REFor mSTING^R231Abut did activate wild-type mSTING and hSTING^THP-1(FIG. 5B). An alternative hypothesis is that cGAS might physically interact with STING and thereby activate STING in a manner independent of cGAMP production. However, this explanation also appears to be incorrect. As previously demonstrated (Sun et al.), overexpression of catalytically dead mutants of human or mouse cGAS failed to activate STING (GS>AA; FIG. 2A), arguing that cGAS signaling depends on the production of a second messenger rather than on a direct physical interaction with STING. To confirm this interpretation, the enzymatic product of cGAS was produced by providing ATP, GTP and dsDNA to purified recombinant cGAS in vitro. As a negative control, dsDNA (required to stimulate cGAS activity) was omitted from a parallel reaction. The resulting cGAS products were then purified and transfected into 293T cells expressing STING variants. In contrast to synthetic cGAMP, the cGAS product was able to activate hSTING^REFand mSTING^R231A(FIG. 5C). This experiment ruled out a model in which cGAS activates hSTING^REFvia a direct physical interaction.
It was therefore hypothesized that the actual product of cGAS might not be a canonical CDN as previously proposed (Sun et al., Wu et al.). It was hypothesized that cGAS might produce a novel CDN containing 2′-5′ phosphodiester bond(s) that would be able to stimulate variant STING alleles. Importantly, such a non-canonical CDN would be of an identical mass to the canonical 3′-5′ phosphodiester-linked CDNs and the two products would not, therefore, have been easy to distinguish by previously published mass spectrometric analyses of the cGAS product (Sun et al., Wu et al.) To test this hypothesis radiolabelled α³²P-GTP or α³²P-ATP were provided to recombinant purified cGAS or V. cholerae DncV and the products were analyzed by thin-layer chromatography. As reported previously, DncV produced some c-di-AMP if provided only ATP, and some c-di-GMP if provided only GTP, but preferred to make cGAMP when provided both ATP and GTP (Davies, et al., Cell (2012)149: 358). (FIG. 6A). Interestingly, cGAS required both ATP and GTP substrates and the resulting product migratessignificantly differently than any of the canonical CDNs produced by DncV,
suggesting that cGAS produces a novel non-canonical CDN (FIG. 6A).
cGAS and DncV products were analyzed by specific nuclease digestion. The cGAS product was partially cleaved by nuclease P1, which selectively digests 3′-5′ phosphodiester linkages, suggesting that the cGAS product contains at least one 3′-5′ phosphodiester linkage (FIG. 6B). However, nuclease P1 digestion was incomplete as it did not lead to generation of GMP, in contrast to treatment of the cGAS product with snake venom phosphodiesterase, which cleaved both 2′-5′ and 3′-5′ phosphodiester linkages (FIG. 3B). This suggests that the cGAS product contains a 2′-5′ phosphodiester linkage.
CDNs have been proposed to be useful as vaccine adjuvants or immunotherapeutics (Chen, et al., Vaccine (2010) 28:3080). A synthetic STING activator, DMXAA, has been tested in human clinical trials as a novel chemotherapeutic agent. Unfortunately, DMXAA was not found to be efficacious in humans, likely because it is unable to stimulate hSTING (Conlon et al.). In this context, our results are significant as they indicate that non-canonical 2′-5′ linked CDNs function as potent pan-agonists of diverse STING variants, including those variants that are only poorly responsive to canonical CDNs or DMXAA.

II. Materials and Methods

A. Mice and Cell Lines

THP-1 cells were grown in RPMI 1640 supplemented with 10% FBS, penicillin-streptomycin and L-glutamine. HEK293T cells were grown in DMEM supplemented with 10% FBS, penicillin-streptomycin and L-glutamine. Gp2 retroviral packaging cell lines were maintained in DMEM supplemented with 10% FBS, penicillin-streptomycin and L-glutamine. Animal protocols were approved by the University of California, Berkeley Animal Care and Use Committee.

B. STING Knockdown

Knockdown of human STING (clone ID NM_—198282.1-90151c1) was achieved using pLKO.1 (The RNAi Consortium). The sequence for knockdown of human STING is 5′-GCA GAG CTA TTT CCT TCC ACA (SEQ ID NO:07) which correspond to 5′-CCG GGC AGA GCT ATT TCC TTC CAC ACT CGA GTG TGG AAG GAA ATA GCT CTG CTT TTT G (SEQ ID NO:08) forward oligo and 5′-AAT TCA AAA AGC AGA GCT ATT TCC TTC CAC ACT CGA GTG TGG AAG GAA ATA GCT CTG C (SEQ ID NO:09) reverse oligo. Oligos were annealed and cloned into Agel and EcoRI digested pLKO.1 (Addgene) and retrovirally transduced into THP-1 cells in parallel with scramble shRNA control constructs. Stable cell lines were selected with puromycin. THP-1 cells were differentiated with 1 μg/mL PMA for 24 hours. Cells were allowed to rest for 24 hours and then restimulated for 6 hours with the indicated ligands. IFN induction was measured by qRT-PCR as described below.

C. Cell Stimulation and Reagents

Bone marrow macrophages and HEK293T cells were stimulated using Lipofectamine 2000 (Invitrogen). Unless otherwise specified, cyclic-di-GMP, cyclic-di-AMP, polyl:C and Vaccinia Virus 70 mer DNA was prepared as described previously (Burdette et al.) and used at similar concentrations. Sendai virus was purchased from Charles River Laboratories. cGAMP was synthesized as previously described (Kellenberger et al).

D. Cloning, Mutagenesis and Plasmids

The THP-1 STING allele was amplified from cDNA using 5′ hSTING HindIII(5′-ATCGAA GCT TCC ACC ATG CCC CAC TCC AGC CTG) (SEQ ID NO:10) and 3′ hSTING NotI (5′-ATC GGC GGC CGC TCA GGC ATA GTC AGG CAC GTC ATA AGG ATA AGA GAA ATC CGT GCG GAG AG) (SEQ ID NO:11). Resulting PCR product was cloned into pCDNA3 using HindIII/NotI digestion. THP-1 STING was amplified and cloned into MSCV2.2 using the 3′ primer listed above and 5′ hSTING XhoI (5′-ATC GCT CGA GCC ACC ATG CCC CAC TCC AGC CTG) (SEQ ID NO:12) and XhoI/NotI digestion. IFN-luciferase, TK-Renilla and mouse STING plasmids were used as previously described (Burdette et al.). Mutations in human STING were introduced using Quikchange Site Directed Mutagenesis Kit (Stratagene). cDNA clones corresponding to mouse and human cGAS (MGC Fully Sequenced Human MB21D1 cDNA, Accession: BC108714.1, Clone ID: 6015929; EST Fully Sequenced Mouse E330016A19Rik cDNA, Accession: BC145653.1, Clone ID: 40130956) were obtained from Open Biosystems and correspond to those described previously (Sun et al., Wu et al.). Mouse cGAS was amplified from cDNA clones with an N-terminal flag tag with forward oligo 5′-mcGAS-KpnI (5′-ATC GGG TAC CCC ACC ATG GAT TAC AAG GAT GAC GAT GAC AAG GAA GAT CCG CGT AGA AGG) (SEQ ID NO:13) and reverse oligo 3′-mcGAS-NotI (5′-ATC GGC GGC CGC TCA AAG CTT GTC AAA AAT TGG) (SEQ ID NO:14). Likewise, hcGAS was amplified with forward oligo 5′-hcGAS-flag-KpnI (5′-ATC GGG TAC CCC ACC ATG GAT TAC AAG GAT GAC GAT GAC AAG CAG CCT TGG CAC GGA AAG G) (SEQ ID NO:15) and reverse 3′-hcGAS-NotI (5′ATC GGC GGC CGC TCA AAA TTC ATC AAA AAC TGG AAA C) (SEQ ID NO:16). Both PCR products were cloned into pCDNA3 at KpnI and NotI restriction enzyme sites. DncV was amplified using DncV fwd BamHI (5′-GCA TGG ATC CGC CAC CAT GAC TTG GAA CTT TCA CCA G) (SEQ ID NO:17) and DncV rev NotI (5′-GCA TGC GGC CGC TCA GCC ACT TAC CAT TGT GCT GC) (SEQ ID NO:18) and cloned into pCDNA3 using BamHI and NotI. For cloning into MSCV2.2, DncV was amplified using DncV fwd XhoI (5′-GCA TCT CGA GCC ACC ATG ACT TGG AAC TTT CAC CAG) (SEQ ID NO:19) and DncV rev NotI. Resulting DNA was cloned into MSCV 2.2 digested with XhoI/NotI. Constructs for bacterial mcGAS overexpression were constructed as follows. N terminal His6-SUMO tag amplified by PCR using His6 SUMO Nco (5′-TAA TAA GGA GAT ATA CCA TGG GCA GCA GCC) (SEQ ID NO:20) and His6 SUMO Sal (5′-GAA TTC GTC GAC ACC AAT CTG TTC TCT GTG AGC) (SEQ ID NO:21) off of pCDF-Duet2 template (gift from M. Rape lab, UC-Berkeley) and cloned into pET28a using NcoI and SalI to make pET28a-H6SUMO. Full length mcGAS was PCR amplified from the mouse cDNA clone described above using mcGAS fwd Sal (5′-GAT GTC GAC ATG GAA GAT CCG CGT AGA AGG ACG) (SEQ ID NO:22) and mcGAS rev Xho (5′-ATC CTC GAG TCA AAG CTT GTC AAA AAT TGG AAA CC) (SEQ ID NO:23) and cloned into pET28a-H6SUMO using SalI and XhoI to make pET28a-H6SUMO-mcGAS that expresses full length mcGAS fused to an N-terminal His6 SUMO tag.

E. Protein Purifications

WspR construct (pQE-WspR*) was a generous gift from Steve Lory (Harvard). WspR purification and c-di-GMP synthesis reactions were carried out as previously described (Merighi, et al., Mol Microbiol (2007)65: 876). Overexpression strains and plasmids for DncV and mutant DncV were provided by J. Mekalanos. DncV protein was overexpressed and purified as previously described (Davies et al.). Briefly, DncV protein production was induced in mid-log phase for 3 h at 37° C. with 1 mM IPTG. Cells were lysed and DncV protein was purified under denaturing conditions. Cleared lysate was incubated with Ni-NTA and eluted in Urea Elution buffer (2M Urea, 10 mM Tris pH=8.0, 150 mM NaCl, 250 mM Imidazole). Eluted protein was dialyzed to 25 mM Tris-Cl, pH=7.5, 300 mM NaCl, 5 mM Mg(OAc)₂, 10% glycerol, 2 mM DTT. H6SUMO-mcGAS was expressed in Rosetta(DE3) pLysS cells by overnight induction with 0.5 mM IPTG at 18° C. Cells were lysed into 50 mM Tris-Cl, pH=8, 300 mM NaCl, 20 mM Imidazole, 5 mM BME and 0.2 mM PMSF by French Press. Cleared lysate was incubated with Ni-NTA and bound protein was eluted with 20 mM Tris-Cl, pH=7.4, 150 mM NaCl, 300 mM Imidazole. Eluant was dialyzed to 20 mM Tris-Cl, pH=7.4, 150 mM NaCl, 5 mM β-mercaptoethanol with 10% glycerol. Protein was flash frozen and stored at −80° C.
F. cGAS Product Purification and Structural Characterization
The cGAS product was purified using reverse-phase HPLC on an Agilent 1260 Infinity HPLC equipped with an Agilent Polaris C18-A column (5 μm, 250 mm×10 mm, 180 Å). Purification conditions include a 100% to 0% gradient of solvent A over 20 min at 50° C. and a flow rate of 5 mL/min, where solvent A is 100 mM ammonium acetate in water and solvent B is acetonitrile. Purified elution fractions were evaporated multiple times in order to remove excess ammonia. Resonance assignments were made using COSY, ¹H-¹³C HSQC, NOESY, ¹H-¹³C HMBC, and 1H-³¹P HMBC. Characterization of cGAS product: ¹H NMR (900 MHz, D2O, 50° C., δ): 8.44 (1H, s), 8.42 (1H, s), 8.03 (1H, s), 6.31 (1H, s), 6.09 (1H, J=8 Hz, d), 5.75 (1H, m), 5.18 (1H, m), 4.93 (1H, s), 4.74, 4.62, 4.59 (1H, J=12 Hz, d), 4.55 (1H, s), 4.38 (1H, m), 4.33 (1H, J=12 Hz, d), 4.28 (1H, J=12 Hz, d); 31P {¹H decoupled} NMR (600 MHz, D20, 50° C., δ): (all resonances are singlets)-0.96, −1.86; HRMS (m/z): [M-H]-monoisotopic mass calculated for C₂₀H₂₄N₁₀O₁₃P₂, 673.0927. found, 673.0909. [M+Na 2H]-monoisotopic mass calculated for C₂₀H₂₄N₁₀O₁₃P₂, 695.0752. found, 695.0728.

G. Luciferase Assay

HEK293T cells were plated in TC-treated 96-well plates at 0.5%°-%106% cells°/0 ml-1. The next day, the cells were transfected with indicated constructs, together with IFN-β-firefly luciferase and TKRenilla luciferase reporter constructs. Following stimulation for 6% h with the indicated ligands, the cells were lysed in passive lysis buffer (Promega) for 5% min at 25° C. The cell lysates were incubated with firefly luciferase substrate (Biosynth) and the Renilla luciferase substrate coelenterazine (Biotium), and luminescence was measured on a SpectraMax L microplate reader (Molecular Devices). The relative lfnb expression was calculated as firefly luminescence relative to Renilla luminescence.

H. In Vitro Cyclic-Di-Nucleotide Synthesis

In vitro DncV reactions were carried out in 20 mM Tris-Cl, pH=8, 20 Mg(OAc)2, 10% glycerol and 1 mM DTT, 0.1 mg/mL BSA. Reactions contained 250 μM GTP, 250 μM ATP or 125 μM GTP and 125 μM ATP as indicated in figures. In addition, 33 nM α32P-GTP (3000Ci/mmol, Perkin-Elmer) or 33 nM α32P-ATP (3000Ci/mmol, Perkin-Elmer) was included in reaction where indicated. Reactions were started by addition of 1 μM purified DncV protein. In vitro cGAS reactions were carried out in 40 mM Tris-Cl, pH=7.5, 100 mM NaCl, 10 mM MgCl2. Cold nucleotide and alpha-labeled GTP is at the same concentrations as in DncV reactions. Reactions were started by addition of 200 nM purified cGAS. Where indicated, herring testes DNA (Sigma) was added to reactions at a final concentration of 0.1 mg/mL. WspR reactions were performed as described previously (14). Reactions were incubated for 1 hour at 37° C., boiled for 5 min at 95° C., and spun for 10 minutes at 13,000 rpm. Reactions were removed and mixed 1:5 with TLC running buffer (1:1.5 (v/v) saturated NH4SO4 and 1.5M KH2PO4, pH 3.6) and spotted on PEIcellulose TLC plate (Sigma). Following solvent migration, the TLC plate was exposed to a phosphorimager screen and imaged using Typhoon scanner. For in vitro product transfection into 293T cells, reactions were scaled up, radiolabeled nucleotide was omitted and the concentration of ATP and GTP was increased to 2 mM.

I. Nuclease Digests

Nuclease P1 from Penicillium citrinum and Snake venom phosphodiesterase I from Crotalus_adamanteus were purchased from Sigma. Reactions from in vitro cyclic-di-nucleotide synthesis labeled with α32P-GTP were diluted 1:5 in either P1 buffer (40 mM Tris-Cl, pH=6, 2 mM ZnCl2) or SVPD buffer (40 mM Tris-Cl, pH=8, mM MgCl2) followed by digestion with 2.5mU of nuclease P1 or SVPD, respectively. Digestions were incubated for 45 minutes at 37° C. and nucleotide products were resolved by TLC.

J. NMR Data

In the ¹H-³¹P HMBC spectrum shown in FIG. 6C, the phosphorous nucleus, P-11, is correlated to the 2′ ribose proton (H-12) of guanosine as well as to the 5′ ribose methylene protons (H-10) and the 4′ ribose proton (H-9) of adenosine. The other phosphorous nucleus (P-22) is correlated to the 3′ ribose proton (H-8) of adenosine as well as to the 5′ ribose methylene protons (H-21) and 4′ ribose proton (H-20) of guanosine. Thus, the regiochemistry of the phosphodiester linkages was determined to be cyclic[G(2′-5′)pA(3′-5′)p]. In order to assign the above peaks, it was critical to accurately identify the ribose spin systems corresponding to guanosine and adenosine, respectively. The protons corresponding to the adenine nucleobase (H-2, H-5) and guanine nucleobase (H-17) were assigned based upon reference spectra for the individual nucleobases, 1H-13C HMBC, and 1H-13C HSQC NMR (FIG. 7A and 7B). The 1H-1H NOESY experiment showed through-space interactions_between the adenine proton H-5 and the 3′ ribose proton (H-8) as well as between the guanine proton H-17 and the 1′ ribose proton (H-18) (FIG. 7D). The remaining protons in the corresponding ribose spin systems were identified by 1H-1H COSY (FIG. 7C), and multiplicity edited 1H-13C HSQC (FIGS. 7A and 7B), which distinguished the 5′ methylene protons in particular (H-10 and H-21).
K. RNA, cDNA Synthesis, and Quantitative RT-PCR
RNA from mammalian cell lines was extracted using Trizol reagent (Invitrogen) or RNeasy Mini Kit (Qiagen). RNA was treated with RQ1 RNase-free DNase (Promega). RNA was reverse transcribed with Superscript III (Invitrogen). Mouse ifnB was quantified relative to mouse rps17 as described previously (Woodward et al). Human ifnB was quantified relative to human S9 as described previously (Wu et al).
The preceding merely illustrates the principles of the invention. It will be appreciated that those skilled in the art will be able to devise various arrangements which, although not explicitly described or shown herein, embody the principles of the invention and are included within its spirit and scope. Furthermore, all examples and conditional language recited herein are principally intended to aid the reader in understanding the principles of the invention and the concepts contributed by the inventors to furthering the art, and are to be construed as being without limitation to such specifically recited examples and conditions. Moreover, all statements herein reciting principles, aspects, and embodiments of the invention as well as specific examples thereof, are intended to encompass both structural and functional equivalents thereof. Additionally, it is intended that such equivalents include both currently known equivalents and equivalents developed in the future, i.e., any elements developed that perform the same function, regardless of structure. The scope of the present invention, therefore, is not intended to be limited to the exemplary embodiments shown and described herein. Rather, the scope and spirit of the present invention is embodied by the appended claims.
All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference. The citation of any publication is for its disclosure prior to the filing date and should not be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention.

Claims

1. A method for increasing the production of a type I interferon (IFN) in a cell, the method comprising:

increasing the level of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide in the cell in a manner sufficient to increase production of the type I interferon (IFN) by the cell.

2. The method according to claim 1, wherein the method comprises contacting the cell with the cyclic-di-nucleotide.

3. The method according to claim 1, wherein the cyclic-di-nucleotide comprises a two 2′-5′ phosphodiester linkage.

4. The method according to claim 3, wherein the cyclic-di-nucleotide comprises a 2′5′ phosphodiester linkage and a 3′-5′ phosphodiester linkage.

5. The method according to claim 1, wherein the cyclic-di-nucleotide comprises a guanosine nucleoside.

6. The method according to claim 5, wherein the cyclic-di-nucleotide comprises two guanosine nucleosides.

7. The method according to claim 1, wherein the cyclic-di-nucleotide comprises an adenosine nucleoside.

8. The method according to claim 7, wherein the cyclic-di-nucleotide comprises two adenosine nucleosides.

9. The method according to claim 1, wherein the cyclic-di-nucleotide comprises an adenosine nucleoside and a guanosine nucleoside.

10. The method according to claim 1, wherein the cyclic-di-nucleotide is described by the formula:

wherein X and Y are each:

11. The method according to claim 10, wherein the cyclic-di-nucleotide is described by the formula:

12. The method according to claim 1, wherein the cyclic-di-nucleotide is described by the formula:

wherein X and Y are each:

13. The method according to claim 1, wherein the level of the cyclic-di-nucleotide is increased by increasing the activity of a cGAMP synthase (cGAS) in the cell.

14-15. (canceled)

16. The method according to claim 1, wherein the IFN is interferon alpha.

17. The method according to claim 1, wherein the IFN is interferon beta.

18. The method according to claim 1, wherein the cell is a mammalian cell.

19. The method according to claim 18, wherein the mammalian cell is a human cell.

20-21. (canceled)

22. A method for increasing the production of a type I interferon (IFN) in a subject, the method comprising:

administering to the subject an amount of a 2′-5′ phosphodiester linkage comprising cyclic-di-nucleotide active agent effective to increase the production of the type I interferon in the subject.

23-42. (canceled)

43. A cyclic-di-nucleotide comprising a 2′-5′ phosphodiester linkage.

44-64. (canceled)

65. A method for increasing a stimulator of interferon genes (STING) mediated response in a subject, the method comprising:

administering to the subject an amount of a STING active agent effective to increase a STING

66-86. (canceled)